In 2005, a study identified conserved elements in the genomes of vertebrates, insects, worms, and yeast. Using a program called phastCons, which is based on a two-state phylogenetic hidden Markov model (phylo-HMM), researchers analyzed multiple alignments of genomes across five vertebrate species, four insect species, two Caenorhabditis species, and seven Saccharomyces species. The predicted conserved elements covered roughly 3%-8% of the human genome, with higher fractions in more compact genomes such as Drosophila melanogaster (37%-53%), Caenorhabditis elegans (18%-37%), and Saccharomyces cerevisiae (47%-68%). These elements showed increasing fractions of conserved bases outside of known protein-coding genes, suggesting the importance of regulatory and noncoding sequences in complex eukaryotes. The most highly conserved elements (HCEs) were hundreds or thousands of bases long and showed extreme levels of conservation but not perfect identity. In vertebrates, HCEs were associated with 3' UTRs of regulatory genes, stable gene deserts, and regions rich in moderately conserved noncoding sequences. Noncoding HCEs also showed strong statistical evidence of an enrichment for RNA secondary structure, consistent with a role in post-transcriptional regulation. The study found that HCEs in vertebrate 3' UTRs and to a lesser extent in 5' UTRs showed strong statistical evidence of an enrichment for local RNA secondary structure. HCEs in introns and intergenic regions also appeared to be enriched for local RNA secondary structure, indicating that many may encode functional RNAs. In vertebrates, intergenic HCEs were strongly enriched in stable gene deserts, suggesting they may act as distal cis-regulatory elements for precisely regulated genes. The study also found that HCEs in 3' UTRs of DNA- and RNA-binding genes such as NOVA1, ELAVL4, ZFHX1B, BCL11A, and SYNCRIP showed extreme conservation, suggesting that regulation in 3' UTRs plays a key role in critical regulatory networks. These findings were consistent with earlier reports of widespread conservation in 3' UTRs. Post-transcriptional regulation by miRNA binding in 3' UTRs was of particular interest, as miRNAs may regulate the translation of a large fraction of eukaryotic genes. The study also found that HCEs in 3' UTRs may be involved in post-transcriptional regulation, possibly through miRNA binding. Additionally, the study found that HCEs in 3' UTRs may be involved in gene regulation via antisense transcription. However, no strong correlation was observed between antisense transcription and extreme conservation in 3' UTRIn 2005, a study identified conserved elements in the genomes of vertebrates, insects, worms, and yeast. Using a program called phastCons, which is based on a two-state phylogenetic hidden Markov model (phylo-HMM), researchers analyzed multiple alignments of genomes across five vertebrate species, four insect species, two Caenorhabditis species, and seven Saccharomyces species. The predicted conserved elements covered roughly 3%-8% of the human genome, with higher fractions in more compact genomes such as Drosophila melanogaster (37%-53%), Caenorhabditis elegans (18%-37%), and Saccharomyces cerevisiae (47%-68%). These elements showed increasing fractions of conserved bases outside of known protein-coding genes, suggesting the importance of regulatory and noncoding sequences in complex eukaryotes. The most highly conserved elements (HCEs) were hundreds or thousands of bases long and showed extreme levels of conservation but not perfect identity. In vertebrates, HCEs were associated with 3' UTRs of regulatory genes, stable gene deserts, and regions rich in moderately conserved noncoding sequences. Noncoding HCEs also showed strong statistical evidence of an enrichment for RNA secondary structure, consistent with a role in post-transcriptional regulation. The study found that HCEs in vertebrate 3' UTRs and to a lesser extent in 5' UTRs showed strong statistical evidence of an enrichment for local RNA secondary structure. HCEs in introns and intergenic regions also appeared to be enriched for local RNA secondary structure, indicating that many may encode functional RNAs. In vertebrates, intergenic HCEs were strongly enriched in stable gene deserts, suggesting they may act as distal cis-regulatory elements for precisely regulated genes. The study also found that HCEs in 3' UTRs of DNA- and RNA-binding genes such as NOVA1, ELAVL4, ZFHX1B, BCL11A, and SYNCRIP showed extreme conservation, suggesting that regulation in 3' UTRs plays a key role in critical regulatory networks. These findings were consistent with earlier reports of widespread conservation in 3' UTRs. Post-transcriptional regulation by miRNA binding in 3' UTRs was of particular interest, as miRNAs may regulate the translation of a large fraction of eukaryotic genes. The study also found that HCEs in 3' UTRs may be involved in post-transcriptional regulation, possibly through miRNA binding. Additionally, the study found that HCEs in 3' UTRs may be involved in gene regulation via antisense transcription. However, no strong correlation was observed between antisense transcription and extreme conservation in 3' UTR