Comprehensive Annotations of Human Herpesvirus 6A and 6B Genomes Reveal Novel and Conserved Genomic Features

Abstract

Human herpesvirus 6 (HHV-6) A and B are highly ubiquitous betaherpesviruses, infecting the majority of the human population. Like other herpesviruses, they encompass large genomes and our understanding of their protein coding potential is far from complete. Here we employ ribosome profiling and systematic transcript analysis to experimentally define the HHV-6 translation products and to follow their temporal expression. We identify hundreds of new open reading frames (ORFs), including many upstream ORFs (uORFs) and internal ORFs (iORFs), generating a complete unbiased atlas of HHV-6 proteome. Furthermore, by integrating systematic data from the prototypic betaherpesvirus, human cytomegalovirus, we uncover numerous uORFs and iORFs that are conserved across betaherpesviruses and we show that uORFs are specifically enriched in late viral genes. Using our transcriptome measurements, we identified three highly abundant HHV-6 encoded long non-coding RNAs (lncRNAs), one of which generates a non-polyadenylated stable intron that appears to be a conserved feature of betaherpesviruses. Overall, our work reveals the complexity of HHV-6 genomes and highlights novel features that are conserved between betaherpesviruses, providing a rich resource for future functional studies.

Parsing the role of NSP1 in SARS-CoV-2 infection

“…Cells were then placed on ice, washed twice with PBS containing 100 μg ml−1 cycloheximide, scraped from 10-cm plates, pelleted and lysed with lysis buffer (1% triton in 20 mM Tris-HCl 7.5, 150 mM NaCl, 5 mM MgCl 2 , 1 mM dithiothreitol supplemented with 10 U/ml Turbo DNase and 100 μg/ml cycloheximide). After lysis, samples stood on ice for 2 h and subsequent ribosome profiling library generation was performed, as previously described(Finkel et al, 2020). In brief, cell lysate was treated with RNase I for 45 min at room temperature followed by SUPERase-In quenching.…”

Dynamic changes in tRNA modifications and abundance during T-cell activation

“…Libraries were sequenced using 75bp single read output run on illumina NEXTseq platform. mRNA-seq for the second biological repeat was done in parallel to ribosome footprint sequencing by a tailored mRNA-sequencing protocol as previously described 61 (see and SI appendix, Extended Material and Methods for further details tRNA sequencing and read analysis tRNA sequencing protocol was adapted from Zheng et al 36 . with minor modification, described in SI appendix, Extended Material and Methods.…”