Transcription and Enhancers
Active transcriptional enhancers are often transcribed into eRNA, the changing levels of which mirror those of the mRNA of the target gene. We discuss some of the reported functions of these RNAs and their likely diversity to allow the utilization of distinct cis-regulatory regions to enhance transcription in various cellular and developmental contexts.
KEYWORDS: chromatin, enhancer, eRNA, histone modification, non-coding RNA, promoter, transcription
Transcription: enhancer and structure of eRNA
High-throughput sequencing studies in recent years have shown that enhancers are often RNAPII-enriched and commonly transcribed. These enhancer RNAs (eRNAs) are generally, but not universally, limited to about 800-2000 bp and arise from the bidirectional transcription of both strands of DNA from a central untranscribed region. Furthermore, they are generally unspliced, only weakly expressed, and lack polyadenylated tails, suggesting a very short half-life. Protein-coding genes often contain putative polyadenylation sites but lack binding sites for small nuclear ribonucleic proteins U1, which appear to block early termination; therefore, eRNAs are not protected against exosome-mediated cleavage and degradation.
Apart from these sequence differences, the chromatin landscape around the transcriptional start sites (TSS) of enhancers also often differs from that seen at proximal promoters and this may also be responsible for some of the differences in sequence. peculiar characteristics of eRNA transcripts. Enhancers are generally enriched for H3K4me1 rather than trimethylation (H3K4me3) commonly seen in promoters of protein-coding genes, the reasons for which are unclear. It was suggested that this simply reflects different rates of transcription, as H3K4me3 is also seen occasionally at enhancers and H3K4me1 sometimes at protein-coding gene start sites.
However, protein-coding genes that are transcribed at low rates do not necessarily have higher ratios of H3K4me1 to K4me3. Enhancers also tend to have particularly high levels of H3K27 acetylation, which is a marker of active chromatin and may also play a role in bidirectionality. At the start sites of protein-coding genes, high levels of histone acetylation correlate with bidirectional transcription, which usually terminates rapidly in the antisense direction. Set2 by phospho-Ser2 RNAPII (pS2-RNAPII), leading to trimethylation of H3K36 (H3K36me3); histone deacetylase (HDAC), Rpd3S, is then recruited by H3K36me3.
In particular, some enhancers are not particularly enriched with pS2-RNAPII and H3K36me3, which could prevent HDAC recruitment to enhancers via a similar mechanism, resulting in a predominantly bidirectional transcription that does not terminate as rapidly due to the sequence elements mentioned above. A very recent publication also suggested a role for WDR82 in limiting these transcripts through Set1 and protein phosphatase 1, both of which appear to play a role in the transcription termination of some lncRNAs.
It is feasible that the genomic and epigenetic landscape in enhancers may also result in different histone modifications because RNAPII is recruited to these elements through a variant preinitiation complex (PIC). TFIID and other general transcription factors were found to be recruited differently from enhancers and promoters, and alternative compositions of PIC complexes were found to be required for gene- and cell-type-specific transcription, and are present in individual cells. from various tissues. Different histone-modifying enzymes in such variant complexes, compared to those associated with the canonical PIC, could also clearly contribute to the divergent patterns of transcription described above.
Flexibility in the use of power-ups
Enhancers are often transcribed in a cell-specific manner and can be highly sensitive to cell state. Cga eRNA levels were found to reflect basal levels of promoter activity, consistent with the report that this enhancer facilitates basal and tissue activity. -specific expression of the CGA gene. This function may be related to the binding of both the enhancer and the proximal promoter by the lineage-specific transcription factor Pitx1, which was found to be associated with several H3K27ac-labeled enhancers of limb genes that are activated during development.
A role for lineage-specific factors has been proposed to enable the regulation of enhancers during development and their ability to determine cell identity by providing control of basic gene expression in a cell-specific manner. tissue. The binding of a particular factor to both the enhancer and the promoter, as Pitx1 does, could also facilitate the physical interactions of these regions; we previously showed that Pitx1 dimerizes and induces conformational changes in DNA upstream of the promoter of the luteinizing hormone β-subunit gene, and other studies also reported that interacting promoter-enhancer pairs contain common TF-binding sites.
The CGA gene is expressed not only in pituitary gonadotropes, but also in thyrotropes, since it is part of the thyrotropin-stimulating hormone, and also in the human blastocyst, where it is part of human chorionic gonadotropin. Pitx1 is not found in both types of cells, and in blastocysts the transcriptional activation of this gene appears to use different regulatory elements, suggesting regulation by different factors and elements in different cell types. In gonadotropes, it is likely that hormonally stimulated Cga gene expression also utilizes additional enhancer elements: even when eRNA knockdown had reduced Cga levels to ~5% compared to wild-type cells, mRNA levels of Cga remained elevated by the primary regulatory hormone, hypothalamic gonadotropin-releasing hormone (GnRH).
In addition, chromatin conformational capture analysis indicated an additional region of interaction in GnRH-treated cells. Also in response to EGF stimulation, different classes of stimulus-induced immediate-early gene-associated enhancers were observed. , and although the DNA loop in response to EGF treatment was abolished by depletion of the integrative complex, the stimulus-independent loop was not affected, indicating a distinct role for different enhancer elements.