Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo

Abstract

The human endogenous retrovirus type-H (HERVH) family is expressed in the preimplantation embryo. A subset of these elements are specifically transcribed in pluripotent stem cells where they appear to exert regulatory activities promoting self-renewal and pluripotency. How HERVH elements achieve such transcriptional specificity remains poorly understood. To uncover the sequence features underlying HERVH transcriptional activity, we performed a phyloregulatory analysis of the long terminal repeats (LTR7) of the HERVH family, which harbor its promoter, using a wealth of regulatory genomics data. We found that the family includes at least 8 previously unrecognized subfamilies that have been active at different timepoints in primate evolution and display distinct expression patterns during human embryonic development. Notably, nearly all HERVH elements transcribed in ESCs belong to one of the youngest subfamilies we dubbed LTR7up. LTR7 sequence evolution was driven by a mixture of mutational processes, including point mutations, duplications, and multiple recombination events between subfamilies, that led to transcription factor binding motif modules characteristic of each subfamily. Using a reporter assay, we show that one such motif, a predicted SOX2/3 binding site unique to LTR7up, is essential for robust promoter activity in induced pluripotent stem cells. Together these findings illuminate the mechanisms by which HERVH diversified its expression pattern during evolution to colonize distinct cellular niches within the human embryo.

Molecular diversity and phenotypic pleiotropy of genomic regulatory loci derived from human endogenous retrovirus type H (HERVH) promoter LTR7 and HERVK promoter LTR5_Hs and their impacts on pathophysiology of Modern Humans

“…Discovery of a complex polyphyletic composition of LTR7 elements comprising of at least eight monophyletic subfamilies (Carter et al, 2022) prompted sequence conservation analyses of each individual monophyletic subfamilies of LTR7 loci in genomes of sixteen NHP. Results of these analyses suggest that diversification of LTR7 loci into genetically and regulatory distinct subfamilies may have occurred early during primate evolution and subsequent cycles of LTR7 expansion appear to faithfully maintain this diversity.…”

“…A total of 3354 LTR7 loci and 606 LTR5_Hs loci residing at fixed non-polymorphic locations in genomes of Modern Humans (hg38 human reference genome database) analyzed in this study were reported previously (Carter et al, 2022; Fuentes et al, 2018). Solely publicly available datasets and resources were used in this contribution.…”

“…Recent investigations of fine molecular structures of LTR7 elements and their genetic and regulatory distinctions demonstrated that LTR7 sequences represent a complex polyphyletic group composed of at least eight monophyletic subfamilies (Carter et al, 2022). Next, sequence conservation analyses of each individual monophyletic subfamilies of LTR7 loci in genomes of sixteen NHP have been performed.…”

“…In contrast, application of a 'phyloregulatory' approach that integrates chromatin state features as well as regulatory and expression profiling genomics data to a phylogenetic analysis of LTR7 sequences facilitated discovery of new insights into the remarkable diversity of origin, evolution, and transcriptional activities of the HERVH/LTR7 family (Carter et al, 2022). This granular interrogation of fine molecular structures of LTR7 elements and their evolutionary history has revealed striking genetic and regulatory distinctions amongst LTR7 elements by demonstrating that LTR7 sequences represent a polyphyletic group composed of at least eight monophyletic subfamilies (Carter et al, 2022).…”

“…Collectively, these findings indicate that the HERVH/LTR7 family underwent the extensive diversification of LTR sequences during primate evolution through a combination of point mutations, indels, and recombination events facilitating the gain, loss, and exchange of multiple cis-regulatory modules. These processes are likely underlying the apparent functional partitioning of LTR7 transcription regulatory activities during primates' preimplantation embryogenesis and maintenance of a pluripotency phenotype (Carter et al, 2022).…”