9.2 Host transcriptomics

Library preparation for host transcriptomics (HT) requires some extra steps to the already described procedures for host genomics and microbial metagenomics. This is due to two main reasons. First, because RNA molecules cannot be directly built into most sequencing libraries, and require instead to generate complementary DNA (cDNA) before library preparation. Second, because gene transcripts tend to be overwhelmingly dominated by rRNA and mtDNA genes, which are often not of interest for the researcher.

Sample quality assessment

Before starting any library preparation protocol assessing the quality of RNA samples is strongly recommended. While traditionally assessed through agarose gel electrophoresis, nowadays RNA quality assessment is performed on electropherogram profiles, which are produced by nucleic acid fragment analysis instruments (e.g. Bioanalyzer, Fragment Analyzer). Traditionally, a simple model evaluating the 28S to 18S rRNA ratio was used as a criterion for RNA quality. However, the most common metric currently employed for assessing the preservation quality of RNA is the RNA integrity number (RIN), which accounts for more RNA features for assessing sample quality [33]. RIN values range from 10 (intact RNA) to 1 (totally degraded RNA). For example, the poly(A) enrichment procedures explained below require high quality RNA (RIN > 8), because RNA degradaation to breaks within the transcript body and due to the selection of the poly(A) tail, the 3’ ends are enriched while the more 5’ sequences would not be captured, leading to a strong 3’ bias for degraded RNA inputs.

DNA removal

Depending on the RNA extraction method employed, it is not rare trace amounts of genomic DNA (gDNA) to be co-purified with RNA. Contaminating gDNA can interfere with reverse transcription and may lead to false positives, higher background, or lower detection in sensitive applications such as RT-qPCR. The traditional method of gDNA removal is the addition of DNase I to RNA extracts. DNase I must be removed prior to cDNA synthesis since any residual enzyme would degrade single-stranded DNA. Unfortunately, RNA loss or damage can occur during DNase I inactivation treatment. As an alternative to DNase I, double-strand–specific DNases are available to eliminate contaminating gDNA without affecting RNA or single-stranded DNAs.

Stranded vs. non-stranded transcriptomics

RNA-Seq libraries can be stranded or non-stranded (unstranded), a decision that affects data analysis and interpretation. Stranded RNA-Seq (also referred to as strand-specific or directional RNA-Seq) enables researchers to determine the orientation of the transcript, whereas this information is lost in non-stranded, or standard, RNA-Seq. Non-stranded RNA-Seq is often sufficient for measuring gene expression in organisms with well-annotated genomes, as with a reference transcriptome, it is possible to infer orientation for most of the sequencing reads. As there are fewer steps than stranded library preparation, the benefits of this approach are lower cost, simpler execution, and greater recovery of material, which renders non-stranded RNA-Seq the preferred option for holo-omic analyses. In contrast, stranded RNA-Seq is useful if the aims include annotating genomes, identifying antisense transcripts or discovering novel transcripts.

cDNA conversion

Most RNA-Seq experiments are carried out on instruments that sequence DNA molecules, rather than RNA. This implies that RNA conversion to cDNA is a required step before library preparation. The synthesis of cDNA from an RNA template is carried out via reverse transcription using reverse transcriptases. In nature, these enzymes convert the viral RNA genome into a complementary DNA (cDNA) molecule, which can integrate into the host’s genome, among other processes.

Reverse transcription, similar to PCR, requires the use of primers. Two main types of primers:

  • Random primers: this type of primers are oligonucleotides with random base sequences. They are often six nucleotides long and are usually referred to as random hexamers. While random primers help improve cDNA synthesis for detection, they are not suitable for full-length reverse transcription of long RNA. Increasing the concentration of random hexamers in reverse transcription reactions improves cDNA yield but results in shorter cDNA fragments due to increased binding at multiple sites on the same template

  • oligo(dT) primers: this type of primers consist of a stretch of 12–18 deoxythymidines that anneal to poly(A) tails of eukaryotic mRNAs (see the section below for further details).

Reverse transcription reactions for cDNA library construction and sequencing involve two main steps: first-strand cDNA synthesis and second-strand cDNA synthesis.

  • First-strand cDNA synthesis: this initial step generates a cDNA:RNA hybrid through the below-described three-step process.

    • Primer annealing: in this step primers are attached to the RNA template, which usually happens before reverse transcriptase and necessary components (e.g., buffer, dNTPs, RNase inhibitor) are added.

    • DNA polymerisation: in this step the complementary DNA is polymerised by the reverse transcriptase enzyme. With oligo(dT) primers (Tm ~35–50°C), the reaction is often incubated directly at the optimal temperature of the reverse transcriptase (37–50°C), while random hexamers typically have lower Tm (~10–15°C) due to their shorter length. Using a thermostable reverse transcriptase allows, a higher reaction temperature (e.g., 50°C), to help denature RNA with high GC content or secondary structures without impacting enzyme activity. With such enzymes, high-temperature incubation can result in an increase in cDNA yield, length, and representation.

    • Enzyme deactivation: in this final step temperature is increased to 70–85°C, depending upon the thermostability of the enzyme, to deactivate the reverse transcriptase.

  • Second-strand cDNA synthesis: in this second step the first-strand cDNA is used as a template to generate double-stranded cDNA representing the RNA targets. Synthesis of double-stranded cDNA often employs a different DNA polymerase to produce the complementary strand of the first cDNA strand.

rRNA depletion through poly-A enrichment

Ribosomal RNA (rRNA) helps translate the information in messenger RNA (mRNA) into protein. It is the predominant form of RNA found in most cells, which can make over 80% of cellular RNA despite never being translated into proteins itself. In consequence, most reads derived from RNA belong to rRNAs, unless depletion strategies are implemented.

Excessively abundant rRNA sequences can be depleted using multiple strategies, which are covered in the Microbial metatranscriptomics. The most broadly employed enrichment strategy when dealing with eukaryotic organisms is rRNA depletion through poly-A enrichment. This strategy relies on the fact that mature coding mRNAs of eukaryotic organisms contain polyA tails, long chains (tens to hundreds) of adenine nucleotides that are added to primary RNA transcripts to increase the stability of the molecule. However, not all transcripts contain poly(A) tails. microRNAs, small nucleolar RNAs (snoRNAs), transfer RNAs (tRNAs), some long non-coding RNAs (lncRNAs), and even protein-coding mRNAs such as histone mRNAs do not contail poly(A) tails, thus will be removed together with rRNA during poly(A) selection. If interested in quantifying expression of such transcripts the use of alternative methods is recommended.

The most broadly employed strategies to deplete rRNA through poly-A enrichment rely either on hybridisation with Oligo(dT)-attached magnetic beads or oligo(dT) priming during cDNA conversion step. In the former strategy, poly(A)-containing RNA molecules hybridise with Oligo(dT) stretches attached to magnetic beads. Following hybridisation, the supernatant consisting of non-polyadenylated molecules is removed. The beads are washed prior to elution of the poly(A)-selected RNA in water or buffer.

List of available protocols

Type Name Author/owner Protocol/Article
oligo(dT) hybridisation Dynabeads Oligo (dT)25-61005 Thermo Fisher Protocol
oligo(dT) priming

Contents of this section were created by Antton Alberdi.


33. Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, et al. The RIN: An RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol. 2006;7:3.