In fact, there are various regulatory mechanisms, which precisely control gene expression. In the following we just want to mention the most common once:
• Promoter: Is a genomic region, where the transcription machinery can bind to transcribe
the following gene into an RNA molecule. Often, promoter regions can be associated
with a high CG content.
• Terminator: Is a genomic region, where the transcription process, and thus the gene
transcript, ends.
• Silencer: A genomic pattern that decreases the frequency of transcription and thus the
expression of the regulated gene.
• Enhancer: A genomic pattern that increases the frequency of transcription and thus the
expression of the regulated gene.
Silencer as well as enhancer DNA can be far from the gene in a linear way; however,
it is spatially close to the promoter and gene. This is managed by folding of the DNA.
• CpG islands: Genomic regions, which are enriched by Cs followed by a G (CpG,
p stands for the phosphate in the DNA backbone). Cytosines in CpG islands can be
methylated, which is an epigenetic regulatory mechanism of gene expression. In most
cases DNA methylation is associated to the inactivation of the corresponding genes.
• Epigenetics: Includes CpG island DNA methylation as mentioned above, but also
histone modifications influencing transcriptional activity.
• UTRs (untranslated regions): The 5’UTR is located before the start codon and the
3’-UTR is the region between the stop codon and the poly-A-tail of the mRNA.
In addition to the regulatory sequences, there are various other sequence components
making up the human genome [12]. The main components are illustrated in Fig. 1.5.
Basically, NGS applications are performed on DNA and RNA molecules. Sequencing
these molecules enables us to identify DNA and RNA sequences but also to define, e.g.,
DNA–protein interactions or epigenetic DNA modifications. Hence, NGS output data give
a great insight into structural and functional characteristics of cells and tissues. Each NGS
application can give a different result, depending on the specific research question. Rapid
DNA and RNA sequencing is now mainstream and will continue to have an increasing
impact on biology and medicine [13].
Common NGS applications are:
• Expression analysis
The RNA-Seq application enables you to investigate expression variances of RNA
structures of, e.g., different tissues. Moreover, RNA-Seq reads can be used to analyze
differential exon usage, gene fusions or variants like SNPs, indels, mutations, etc. [14].
• DNA–protein interactions
The ChIP-Seq (chromatin-immunoprecipitation) application focuses on investigating
regulatory sequences of the DNA, like transcription factor binding sites or histone
modifications (e.g., acetylation/methylation), which lead to differences in gene
1 Next Generation Sequencing (NGS): What Can Be Sequenced?
9
• Promoter: Is a genomic region, where the transcription machinery can bind to transcribe
the following gene into an RNA molecule. Often, promoter regions can be associated
with a high CG content.
• Terminator: Is a genomic region, where the transcription process, and thus the gene
transcript, ends.
• Silencer: A genomic pattern that decreases the frequency of transcription and thus the
expression of the regulated gene.
• Enhancer: A genomic pattern that increases the frequency of transcription and thus the
expression of the regulated gene.
Silencer as well as enhancer DNA can be far from the gene in a linear way; however,
it is spatially close to the promoter and gene. This is managed by folding of the DNA.
• CpG islands: Genomic regions, which are enriched by Cs followed by a G (CpG,
p stands for the phosphate in the DNA backbone). Cytosines in CpG islands can be
methylated, which is an epigenetic regulatory mechanism of gene expression. In most
cases DNA methylation is associated to the inactivation of the corresponding genes.
• Epigenetics: Includes CpG island DNA methylation as mentioned above, but also
histone modifications influencing transcriptional activity.
• UTRs (untranslated regions): The 5’UTR is located before the start codon and the
3’-UTR is the region between the stop codon and the poly-A-tail of the mRNA.
In addition to the regulatory sequences, there are various other sequence components
making up the human genome [12]. The main components are illustrated in Fig. 1.5.
Basically, NGS applications are performed on DNA and RNA molecules. Sequencing
these molecules enables us to identify DNA and RNA sequences but also to define, e.g.,
DNA–protein interactions or epigenetic DNA modifications. Hence, NGS output data give
a great insight into structural and functional characteristics of cells and tissues. Each NGS
application can give a different result, depending on the specific research question. Rapid
DNA and RNA sequencing is now mainstream and will continue to have an increasing
impact on biology and medicine [13].
Common NGS applications are:
• Expression analysis
The RNA-Seq application enables you to investigate expression variances of RNA
structures of, e.g., different tissues. Moreover, RNA-Seq reads can be used to analyze
differential exon usage, gene fusions or variants like SNPs, indels, mutations, etc. [14].
• DNA–protein interactions
The ChIP-Seq (chromatin-immunoprecipitation) application focuses on investigating
regulatory sequences of the DNA, like transcription factor binding sites or histone
modifications (e.g., acetylation/methylation), which lead to differences in gene
1 Next Generation Sequencing (NGS): What Can Be Sequenced?
9