Adenine is one of the four bases (letters) of DNA.
Agrobacterium is a soil bacterium that can naturally infect plants and cause tumor-like growths in plants. The Agrobacterium is used as a molecular tool to produce genetically modified plants. The genetic information for the growths is on a piece of extra DNA that is arranged in a ring, called a plasmid. This is transmitted into the cell by the bacterium when the plant is infected. The so-called T-DNA (with the genetic information for the growths) is then incorporated at any point in the genome. Scientists use the bacterium as a transport vector to introduce genes that they incorporate into the T-DNA into plants. Instead of building in the genetic information for the growths, genes are built in that the scientist would like to introduce into the plant cells.
Amino acids are the individual building blocks of proteins. Amino acids are organic compounds that differ in specific side groups. There are 20 different amino acids that can be linked to one another in a chain-like manner in proteins.
Bases are organic molecules that are important components of DNA and RNA. They are often referred to as the letters of DNA. The array of the bases determines the sequence of the DNA (the genetic code). The four nucleobases adenine (A), guanine (G), cytosine (C) and thymine (T) are used in DNA.
The opposite bases on the double strand of the DNA are referred to as base pairs or letters of the DNA.
Biolistic procedures are among the methods of old genetic engineering. In this process, pieces of DNA are applied to small beads and shot directly into the nucleus of a cell. The synthetic DNA fragments can then be incorporated into the genome.
The cell cycle can be divided into 4 phases: cell division (mitosis), G1 phase, S phase (replication) and G2 phase. Between two cell divisions, cells of higher living beings go through different phases. After cell division, the DNA content is reduced. In the course of the cell cycle, the DNA is doubled and the cells prepare for the next cell division by producing proteins.
The genetic information of an organism is located on the chromosomes. A chromosome consists of the cell nucleus DNA and various proteins. Chromosomes are the condensed form of the DNA in the nucleus of a cell.
In conventional mutagenesis, ionizing radiation or chemical substances (physical and chemical mutagens) are used in plant breeding to generate mutations. This enhances the spontaneous mutation rate in the genome and increases the genetic diversity, which is the starting point for further breeding.
Conventional plant breeding
The aim of conventional plant breeding is to change or improve the properties of plants. Plants with certain properties are selected, crossed with one another and the plants of the next generation are then selected for the desired properties. These plants can then be used for the next breeding cycle. Physical or chemical mutagens are often used to increase genetic diversity at the beginning of the selection process.
CpG islands are short DNA sequences in the genome of humans and animals that are particularly rich in the bases cytosine and guanine.
CRISPR/Cas is the abbreviation for Clustered regularly interspaced palindromic repeats/CRISPR associated. CRISPR are small regions of bacterial DNA that aid in the immune defense against invading viruses. Cas is the cutting component of the CRISPR/Cas system (i.e. nuclease) and cuts the double strand at the target region of the DNA. The CRISPR/Cas system was adopted from the bacteria as a molecular biological technology and modified in such a way that the genome of other organisms such as plants and animals can be modified as specifically as possible in the laboratory.
Crossing-over is a process during the maturation of the germ cells. Pieces of homologous chromosomes (these are structurally identical chromosomes of paternal and maternal origin with the same array of gene locations) are exchanged. The result is a recombination of parental properties.
Cytosine is one of the four bases (letters) of DNA.
DNA stands for deoxyribonucleic acid. DNA is a macromolecule that carries genetic information. It consists of nucleotides. The DNA forms a double strand wound like a helix.
During the methylation of DNA a chemical molecule, a methyl group, is attached to the DNA. The methyl group consists of one carbon and three hydrogen atoms.
Methyltransferases are enzymes that transfer methyl groups to the bases in DNA.
The genetic information of humans, animals and plants is made up of two long, filamentous DNA molecules (two DNA strands), which are linked to one another by cross-connections (base pairing through the formation of hydrogen bonds).
Plants, but also animals, were bred by humans over many centuries in order to adapt them especially for human consumption. This process is called domestication.
Plants with a single set of chromosomes are called haploid. For example, haploid plants can be produced from immature pollen with the aid of a suitable culture medium. By adding the cell division inhibitor colchicine, the chromosomes are doubled. The plant then has two sets of chromosomes and is called double haploid in contrast to normal diploid plants. The plants are homozygous in terms of their properties.
Enzymes are proteins that have a specific function and implement a reaction inside of cells. They are often referred to as bio-catalysts.
Epigenetics describes mechanisms and, in some cases, hereditary changes in the genome that are not based on changes in the DNA sequence and have an impact on the phenotype of an organism. Among other things, epigenetics regulates the activity of genes, for example during the development of living beings or in response to the environment.
Epigenetic markers refer to small appendages to the DNA and also to proteins to which the DNA is attached (called histones). They regulate gene expression within the cells.
The epigenome describes the sum of all epigenetic states in a cell.
A gene is divided into several parts, the exons and introns. Exons are areas of a gene that are actually used for translation into the respective protein. The areas in between, also called introns, are cut out in a process called “splicing” and are not used to make proteins.
A gene is a section of DNA that carries information for the development of characteristics of an individual and is used for the formation of RNA, which is then translated into a protein.
Gene clusters describe DNA areas, where genes are present in increased copy numbers.
Gene drives are techniques that ensure the rapid spreading of genes within a wild population. The genetic traits are inherited more frequently than genes that are inherited according to Mendelian rules. Genetically engineered gene drives can increase heredity to the next generation by up to 100 percent.
The process of using gene information for the synthesis of a functional gene product is called gene expression and is a prerequisite for gene activity.
Members of a gene family are genes that are very similar in their DNA sequence and functions.
Gene regulation refers to the regulation of the switching on and off of genes, i.e. the control of gene expression.
Several, identical DNA sequences of a gene in the genome are called gene copies.
A gene knock-out is a change of the gene sequence in the genome of an organism switching off the respective gene. The corresponding protein can then no longer be formed.
Gene scissors are enzymes, more specifically nucleases. The term gene scissors is often used for the targeted nuclease CRISPR/Cas9 to convey how it works in simple words. Other nucleases are TALENs or zinc finger nucleases. The gene scissors cut at certain regions of the genome and often cause a change within a target region.
If genes are located in close proximity on a chromosome, they are very likely inherited together, so they are genetically linked to one another.
The genome describes the entirety of the DNA of an individual that is found in the cell nucleus of plants and animals.
Genome editing are molecular biological techniques that are intended to change the genome of an organism (humans, animals, plants) in a targeted way. These techniques include among others site-directed nucleases (also known as gene scissors). In contrast to transgenic organisms, genes do not necessarily have to be transferred across species.
Genomics include techniques to analyze the DNA sequence of the genome of an organism.
Genome sequencing determines the exact sequence of the bases in the genome of an organism.
The genotype describes the sum of genetic material of an individual.
Guanine is one of the four bases (letters) of DNA.
The guide RNA (gRNA) is a short RNA molecule that leads the gene scissors CRISPR/Cas to the target region on the genome to be changed. The gRNA is able to recognize the DNA-sequence of the target region, to bind it and to bring the gene scissors into the correct position for cutting. The guide RNA is the recognition component of the gene scissors.
HDR is the abbreviation for homology directed repair and describes a natural repair mechanism with which double-strand breaks in the DNA is repaired by similar (homologous), double-stranded DNA molecules.
Histones are proteins and components of chromatin with which the DNA is packaged in the cell nucleus and play an important role in the regulation of gene expression.
In the cells of higher plants and animals, chromosomes exist in multiple copies (usually two chromosome pairs (diploid), but some plants have more than two paired sets of chromosomes (polyploid)). The homologous, identical chromosomes match each other in terms of shape, structure and gene sequence.
InDels is the abbreviation for insertions and deletions. Insertions are the incorporation of additional nucleotides into the DNA sequence and deletions are the loss of a DNA region.
In-silico describes processes that are simulated on the computer using special programs. It can be used, for example, to calculate where in the genome DNA sequences that are very similar, are located. In this way, areas in the genome can be identified that are very similar to a target sequence of the gene scissors and where off-target effects are likely to occur.
Lipidomics processes examine the composition of fats and are part of metabolomics.
Mass spectrometry refers to methods of measuring the mass of molecules.
The metabolism comprises chemical reactions in an organism that are involved in the construction, degradation and remodeling processes inside of cells.
The metabolism consists of many individual steps in which specific products are created through enzymatic conversions. These metabolic products are called metabolites.
With the use of metabolomic techniques the composition of all components in the metabolism (metabolites) of cells and tissues can be examined.
A methyl group is an organic molecule made up of one carbon and three hydrogen atoms. The methyl group does not appear alone as a substance, but is attached to other molecules. Methylation of DNA controls gene expression and is one of the cell’s epigenetic processes. In DNA methylation, a methyl group is attached to the base cytosine in certain areas in the genome and thus gene expression is regulated.
The microbiome of multicellular organisms (humans, animals, plants) comprises the entirety of all microorganisms that naturally colonize such an organism. In humans, the number of microorganisms in the intestine is actually higher than the number of cells in the body. Microbiomes and their “hosts” exchange nutrients and biologically active molecules with one another and can also influence one another’s gene regulation.
By using several guide RNAs it is possible to change multiple (different) target regions of the genome at the same time. But even if only one guide RNA is used, several genomic regions can be changed at once, since genes are often present in several copies in the genome.
Mutagens are substances that can be used to increase the occurrence of mutations in the genome. These are usually chemical or physical (i.e. unspecific) stimuli.
Mutagenesis describes the generation of mutations in the genome of living beings, although it is important to distinguish how these mutations were induced: on the one hand, mutations occur spontaneously; on the other hand, mutations for research or breeding purposes are generated by the treatment of chemical substances or physical radiation. The use of CRISPR/Cas is sometimes also referred to as mutagenesis, but these biotechnological processes differ significantly from conventional mutagenesis in terms of their specific mode of action.
mRNA (messenger RNA)
The messenger RNA is a single-stranded RNA that carries genetic information for the construction of a protein. It is created by reading genes. mRNA is formed in the cell nucleus and converted into proteins in the cytoplasm.
New genetic engineering
New genetic engineering techniques (for example CRISPR/Cas9, TALENs or zinc finger nucleases) enable the change of genetic information of an organism (humans, animals, plants) in a targeted way.
NHEJ is the abbreviation for non-homologous end joining and is the name of a cell’s own repair mechanism. With the NHEJ repair, double-strand breaks in the DNA are reassembled. This mechanism is sometimes prone to errors, i.e. the original state can be restored or small changes can be induced in the DNA sequence. The aim of the NHEJ repair is to close DNA double-strand breaks in the genome as quickly as possible.
Nuclear Magnetic Resonance Spectroscopy (NMR Spectroscopy)
Nuclear magnetic resonance spectroscopy is a method with which the structure of proteins or metabolic products can be clarified.
A nuclease is an enzyme that can cut DNA causing DNA double-strand breaks in the genome and is often referred to as genetic scissors.
A nucleotide is made up of three components:
- Base – one of the five bases, adenine (A), guanine (G), cytosine (C), thymine (T) (for DNA) or uracil (U) (instead of thymine, for RNA).
- Sugar – in this case, carbon atoms arranged in a ring formation, classified as ribose or deoxyribose
- a phosphate group
Old genetic engineering
The old genetic engineering describes various methods (e.g. biolistic processes or use of Agrobacterium tumefaciens) with which it is possible to introduce DNA into organisms or cells and incorporate it into their genome. The methods of the old genetic engineering are often used to introduce the tools of the new genetic engineering (i.e. genome editing) into the cells.
Omics examine the entirety of certain components of the cell. In genomics, for example, the entirety of DNA is examined; in proteomics, the entirety of all proteins within a cell.
On-target refers to the target region of the DNA that is intended to be changed by site-directed nucleases.
On-target effects are unintended alterations that affect the area around the target region of an SDN application. This can be, for example, unintended rearrangements at the target site as well as unintended integration of additional gene scissor DNA fragments.
Regions of the genome that are not in direct proximity to the target region of the site-directed nuclease, are referred to as off-target.
Off-target effects are unintended alterations, that can arise when the gene scissors cut at unintended regions of the genome. Often these DNA regions are very similar to the target sequence and the gene scissors confuse the off-target sites with the actual target sequence.
PAM stands for protospacer adjacent motif and is a DNA sequence, which serves as a recognition and binding site for the CRISPR/Cas system. It lies in front of the actual target site of the DNA.
PCR (polymerase chain reaction) is an analytical method used in the laboratory with which known DNA sequences can be detected in a DNA sample in a short time frame.
A phenotype describes the appearance of an organism that is shaped by both hereditary factors and environmental influences.
Plasmids consist of DNA arranged as a ring, which is found in bacteria in addition to their chromosomal DNA. Plasmids are used by bacteria to transfer genetic information between them and are small, usually circular, self-replicating double-stranded DNA molecules that exist in bacteria, but are not integrated into the bacterial chromosomes. Plasmids can contain different genes, for example genes that can confer resistance to antibiotics. These resistances can be exchanged between bacteria by the exchange of these plasmids. So-called Ti (tumor inducing) plasmids are found in the species Agrobacterium tumefaciens and Agrobacterium rhizogenes and can be transferred into plants.
Plasmids are important tools in genetic engineering. They are also known as vectors and are used to reproduce or transfer genes. Ti plasmids, for example, are used to transfer genes in plant cells. The DNA encoding the gene scissors, for example, can be introduced into a cell.
Polyploidy means that there are more than two chromosome sets in the nucleus of an organism. Polyploidy is common in plants, such as corn, which has six chromosome sets and is hexaploid.
A population comprises the totality of all individuals of a species that live in one place.
Proteins are large biomolecules and consist of amino acids that are linked together. Proteins have diverse structures and can therefore have different functions in the cell. For example, they have important functions in the metabolism, during cellular transport of signaling substances and enable cellular movement.
In proteomics, the composition of all proteins in cells and tissues is examined.
A protoplast is a plant cell without a cell wall. Animal cells generally do not have a cell wall.
RNA stands for ribonucleic acid. Similiar to DNA it also consists of nucleotides, but it contains the base uracil instead of thymine, which is a building block of DNA. The sugar component of RNA is different from that of DNA, namely ribose instead of deoxyribose. RNA has important functions as a link in the translation of genes into proteins and also has important regulatory functions in the cell (in the context of epigenetics).
SDN stands for site-directed nucleases and combines techniques such as CRISPR/Cas9, TALENs and zinc finger nucleases that are intended to cause changes within a target region of the genome.
Site-directed nuclease-1 (SDN-1) describes applications of targeted nucleases like CRISPR/Cas, that are introduced into a cell causing a double-strand break at a target region of the DNA. These double-strand breaks activate repair mechanisms in the cell, which introduce changes in the target sequence. No DNA templates are brought into the cell for the repair of the DNA double strand break in SDN-1 applications.
In contrast to SDN-1, site directed nuclease-2 (SDN-2) applications use small pieces of DNA (a few base pairs long) that are produced in the laboratory and additionally introduced into the cell. The DNA pieces serve as repair templates for the DNA double strand break. Scientist are able to introduce specific changes to the target sequence by using DNA donor templates.
Large pieces of DNA (e.g. entire gene regions) can also be introduced into the cell together with the CRISPR/Cas system and specifically incorporated into the target region surrounding the DNA double strand break. This type of application is summarized under site directed nuclease-3 (SDN-3).
Sets of chromosomes
In the nucleus of a cell, the chromosomes can exist in different amounts. For example, humans have a diploid pair of chromosomes with 23 chromosomes coming from the mother and 23 from the father.
TALENs are transcription activator-like effector nucleases, which belong to the site-directed nucleases of genome editing techniques.
The DNA sequence that is to be modified by site-directed nucleases is known as the target region. It is recognized, for example, by the guide RNA during the application of CRISPR/Cas and then cut by the gene scissors.
Thymine is one of the four bases (letters) of DNA.
Transcriptomics are processes with which one can determine all RNA molecules within a cell at a certain point in time.
Transgenic organisms are organisms in which one or more genes, that do not originate from their own species, have been inserted into the genome using genetic engineering techniques.
Transgenic plants carry foreign genes in their genomes that were introduced using genetic engineering methods.
The entirety of all RNA molecules within a cell or a tissue.
A translocation is a shift of DNA sequences within the same chromosome or from one chromosome to another.
Transposons (“jumping genes”) are DNA sequences that can change their position within the genome. Transposons are among the most common ‘egoistic’ elements in the genome. Essentially, they only consist of an enzyme that makes copies of the transposon and inserts them into another part of the genome. Transposons occur in humans, animals, plants and bacteria. In their mode of action and their structure, transposons are similar to viruses that incorporate their viral genetic material into the genome of their hosts. There are many different types of transposons in each organism.
Uracil is one of the four bases (letters) of RNA.
Whole genome sequencing
Whole genome sequencing are high-troughput DNA sequencing techniques that decode the entire genome with the exact sequence of the bases.
Zinc finger nucleases
Zinc finger nucleases are site-directed nucleases. The zinc finger domain binds to a specific target region of the DNA, and then the nuclease domain cuts the DNA.
As of April 2021