1986/01/01 by B. Silver, Courtney G. Willett, Kelsey A. Maher +3 · 1 voice
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Social Sciences · #Demographic Trends and Gender Preferences #Genomics and Chromatin Dynamics #Migration and Labor Dynamics #Plant Molecular Biology Research #RNA and protein synthesis mechanisms
paper · pdf · doi:10.1101/2023.11.03.565513
openalex publication_date 1986/01/01 · openalex created_date 2016/06/24 · openalex updated_date 2026/04/28
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene expression. High-throughput profiling of fungal and animal genomes has revealed that RNA Polymerase II (Pol II) often initiates transcription in both directions at the promoter transcription start site (TSS), but generally only elongates productively into the gene body. Additionally, Pol II can initiate transcription in both directions at cis-regulatory elements (CREs) such as enhancers. These bidirectional Pol II initiation events can be observed directly with methods that capture nascent transcripts, and they are also revealed indirectly by the presence of transcription-associated histone modifications on both sides of the TSS or CRE. Previous studies have shown that nascent RNAs and transcription-associated histone modifications in the model plant <i>Arabidopsis thaliana</i> accumulate mainly in the gene body, suggesting that transcription does not initiate widely in the upstream direction from genes in this plant. We compared transcription-associated histone modifications and nascent transcripts at both TSSs and CREs in <i>Arabidopsis thaliana</i>, <i>Drosophila melanogaster</i>, and <i>Homo sapiens</i>. Our results provide evidence for mostly unidirectional Pol II initiation at both promoters and gene-proximal CREs of <i>Arabidopsis thaliana</i>, whereas bidirectional transcription initiation is observed widely at promoters in both <i>Drosophila melanogaster</i> and <i>Homo sapiens,</i> as well as CREs in <i>Drosophila</i>. Furthermore, the distribution of transcription-associated histone modifications around TSSs in the <i>Oryza sativa</i> (rice) and <i>Glycine max</i> (soybean) genomes suggests that unidirectional transcription initiation is the norm in these genomes as well. These results suggest that there are fundamental differences in transcriptional initiation directionality between flowering plant and metazoan genomes, which are manifested as distinct patterns of chromatin modifications around RNA polymerase initiation sites.