Updated mapping and proposed new annotation of the HHV-6B transcriptome

A group led by Louis Flamand at Laval University in Canada performed large-scale RNA sequencing to analyze the HHV-6B transcriptome during different time points over 72 hours during productive infection of human Molt-3 T-cells. Many of the transcripts were confirmed via reverse transcriptase PCR and Sanger sequencing.

For most of the genome, a read coverage of 100x was obtained. Other regions, such as the telomeric repeat regions, R2 and R3, showed less than 1x or no coverage, indicating that they are not efficiently transcribed.

Differential expression of new HHV-6B transcripts was observed in all samples analyzed.

U90 (IE1) was expressed in abundance throughout the entire time course of the infection. In contrast, there were also many time-dependent genes, such as U27, which began expression at 9 hours post-infection, and DR6, which was expressed 48 hours post-infection. The researchers were able to match transcripts from the majority of open reading frames to a particular kinetic class (e.g., immediate-early, early, and late genes).

Some regions were transcribed in a forward direction, and some in a reverse direction. The team reports substantial evidence of new splice variants of previously reported open reading frames (ORFs), including some transcripts that have yet to be defined.

Of special interest, the RNA-seq data obtained for the region spanning U44 to U46 contained many reads and splicing events. The U44 and U46 genes were transcribed in the 59 to 39 direction, whereas the U45 gene was transcribed in the reverse direction (Fig. 7A). No intron was described for these three genes in either HHV-6B or HHV-6A (Fig. 7A).

Overall, the work demonstrates the diversity and the complexity of the HHV-6B transcriptome. In addition, the investigators have proposed an updated version of the HHV-6B Z29 GenBank annotated genome file, without changing ORF names, to facilitate correlation of their work with previous studies on HHV-6B. This updated version has been deposited under GenBank accession number MW536483

Read the full article: Gravel 2021