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Genome‐Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease

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ABSTRACT

Gene expression is regulated by numerous elements including enhancers, insulators, transcription factors, and architectural proteins. Regions of DNA distal to the transcriptional start site, called enhancers, play a central role in the temporal and tissue‐specific regulation of gene expression through RNA polymerase II. The identification of enhancers and other cis regulatory elements has largely been possible due to advances in next generation sequencing technologies. Enhancers regulate gene expression through chromatin loops mediated by architectural proteins such as YY1, CTCF, the cohesin complex, and LDB1. Additionally, enhancers can be transcribed to produce noncoding RNAs termed enhancer RNAs that likely participate in transcriptional regulation. The central role of enhancers in regulating gene expression implicates them in both normal physiology but also many disease states. The importance of enhancers is evident by the suggested role of SNPs, duplications, and other alterations of enhancer function in many diseases, ranging from cancer to atherosclerosis to chronic kidney disease. Although much progress has been made in recent years, the field of enhancer biology and our knowledge of the cis regulome remains a work in progress. This review will highlight recent seminal studies which demonstrate the role of enhancers in normal physiology and disease pathogenesis. © 2019 American Physiological Society. Compr Physiol 9:439‐455, 2019.

Figure 1. Figure 1. Trans factors involved in chromatin looping.YY1 dimerization increases chromatin looping and enhancer‐promoter interactionCohesin and CTCF are enriched at chromatin loop anchorsLDB1 is enriched at the loop anchors at the β‐globin locus
Figure 2. Figure 2. Enhancers versus promoters.Enhancers function independent of orientation. If an enhancer is flipped, it maintains its gene regulation function. A flipped promoter, however, will block gene transcription.Enhancers function independent of location. An enhancer that is moved downstream or upstream remains functional. A promoter that is no longer directly adjacent to the TSS will not drive transcription.
Figure 3. Figure 3. Characteristic histone marks.Active promoter: H3K4me3Poised enhancer: H3K4me1, H3K27me3Active enhancer: H3K4me1, H3K27acSilenced region: H3K9me2 or H3K9me3
Figure 4. Figure 4. Enhancers and RNA polymerase II. Proteins, such as Paf1, JMDJ6, BRD4, or others, bind enhancers, and promote PTEFb‐mediated phosphorylation of NELF (negative elongation factor), DSIF (DRB sensitive inducing factor) and RNA pol II. RNA pol II is released, and transcriptional elongation occurs.
Figure 5. Figure 5. eRNAsChIP‐Seq analysis identifies eRNA producing enhancers by enrichment for H3K27Ac and RNA pol IIModel of eRNA function at Nanog function. eRNAs appear to facilitate or stabilize chromatin loops between specific enhancer:gene promoter combinations.
Figure 6. Figure 6. Proposed models of alteration of enhancer function leads to cancer development.Activation of enhancers results in the opening of chromatin, leading to the greater likelihood of chromosomal rearrangements that ultimately lead to aneuploidy ().Duplication of enhancer sequences that regulate MYC leads to increased MYC expression that drives epithelial cancers ().Translocation of G2DHE (a GATA2 enhancer) near the EVI1 locus leads to overexpression of the EVI1 oncogene, promoting myeloid and B‐cell leukemic development ().Heterozygous loss of cohesin leads to changes in nuclear architecture that can alter enhancer‐promoter interactions and lead to gene expression changes that promote myeloid transformation.


Figure 1. Trans factors involved in chromatin looping.YY1 dimerization increases chromatin looping and enhancer‐promoter interactionCohesin and CTCF are enriched at chromatin loop anchorsLDB1 is enriched at the loop anchors at the β‐globin locus


Figure 2. Enhancers versus promoters.Enhancers function independent of orientation. If an enhancer is flipped, it maintains its gene regulation function. A flipped promoter, however, will block gene transcription.Enhancers function independent of location. An enhancer that is moved downstream or upstream remains functional. A promoter that is no longer directly adjacent to the TSS will not drive transcription.


Figure 3. Characteristic histone marks.Active promoter: H3K4me3Poised enhancer: H3K4me1, H3K27me3Active enhancer: H3K4me1, H3K27acSilenced region: H3K9me2 or H3K9me3


Figure 4. Enhancers and RNA polymerase II. Proteins, such as Paf1, JMDJ6, BRD4, or others, bind enhancers, and promote PTEFb‐mediated phosphorylation of NELF (negative elongation factor), DSIF (DRB sensitive inducing factor) and RNA pol II. RNA pol II is released, and transcriptional elongation occurs.


Figure 5. eRNAsChIP‐Seq analysis identifies eRNA producing enhancers by enrichment for H3K27Ac and RNA pol IIModel of eRNA function at Nanog function. eRNAs appear to facilitate or stabilize chromatin loops between specific enhancer:gene promoter combinations.


Figure 6. Proposed models of alteration of enhancer function leads to cancer development.Activation of enhancers results in the opening of chromatin, leading to the greater likelihood of chromosomal rearrangements that ultimately lead to aneuploidy ().Duplication of enhancer sequences that regulate MYC leads to increased MYC expression that drives epithelial cancers ().Translocation of G2DHE (a GATA2 enhancer) near the EVI1 locus leads to overexpression of the EVI1 oncogene, promoting myeloid and B‐cell leukemic development ().Heterozygous loss of cohesin leads to changes in nuclear architecture that can alter enhancer‐promoter interactions and lead to gene expression changes that promote myeloid transformation.
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Teaching Material

P. Agrawal, K. E. Heimbruch, S. Rao. Genome-Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease. Compr Physiol 9: 2019, 469-485.

Didactic Synopsis

Major Teaching Points:

  • Transcriptional regulation is a complex process controlled by numerous elements, which act either in cis or trans.
  • Enhancers are DNA elements containing transcription factor binding motifs that play an important role in transcriptional regulation in a distance and orientation independent manner.
  • Technological advances have been essential in identifying enhancers and their role in regulating gene expression.
  • Enhancers regulate gene expression through interactions with RNA polymerase II by regulating transcriptional elongation.
  • Enhancers operate by being in close physical proximity to the genes they regulate within the nucleus. This is mediated by chromatin looping mediated by architectural proteins such as YY1, CTCF, LDB1, and the cohesin complex.
  • SNPs, duplications, and other alterations in enhancer function have been implicated in a wide variety of diseases.

Didactic Legends

The figures—in a freely downloadable PowerPoint format—can be found on the Images tab along with the formal legends published in the article. The following legends to the same figures are written to be useful for teaching.

Figure 1 Trans factors involved in chromatin looping. (A) YY1 dimerization increases chromatin looping and enhancer-promoter interaction (B) Cohesin and CTCF are enriched at chromatin loop anchors (C) LDB1 is enriched at the loop anchors at the β-globin locus Teaching point: Chromatin looping may be due to multiple different mechanisms

Figure 2 Enhancers versus promoters. (A) Enhancers function independent of orientation. If an enhancer is flipped, it maintains its gene regulation function. A flipped promoter, however, will block gene transcription. (B) Enhancers function independent of location. An enhancer that is moved downstream or upstream remains functional. A promoter that is no longer directly adjacent to the TSS will not drive transcription. Teaching point: Enhancers function independent of orientation and location, unlike promoters.

Figure 3 Characteristic histone marks. (A) Active promoter: H3K4me3 (B) Poised enhancer: H3K4me1, H3K27me3 (C) Active enhancer: H3K4me1, H3K27ac (D) Silenced region: H3K9me2 or H3K9me3 Teaching point: the activity or lack thereof of enhancers can be inferred by various histone marks.

Figure 4 Enhancers and RNA polymerase II. Proteins, such as Paf1, JMDJ6, BRD4 or others, bind enhancers, and promote PTEFb-mediated phosphorylation of NELF (negative elongation factor), DSIF (DRB sensitive inducing factor) and RNA pol II. RNA pol II is released, and transcriptional elongation occurs. Teaching point: Enhancers interact with proteins allowing conversion from transcriptional initiation to elongation.

Figure 5 eRNAs. (A) ChIP-Seq analysis identifies eRNA producing enhancers by enrichment for H3K27Ac and RNA pol II. (B) Model of eRNA function at Nanog function. eRNAs appear to facilitate or stabilize chromatin loops between specific enhancer:gene promoter combinations. Teaching Point: eRNAs can be identified through ChIP-Seq analysis and may play a role in regulation gene expression changes.

Figure 6 Proposed models of alteration of enhancer function leads to cancer development. (A) Activation of enhancers results in the opening of chromatin, leading to the greater likelihood of chromosomal rearrangements that ultimately lead to aneuploidy (21). (B) Duplication of enhancer sequences that regulate MYC leads to increased MYC expression that drives epithelial cancers (121). (C) Translocation of G2DHE (a GATA2 enhancer) near the EVI1 locus leads to overexpression of the EVI1 oncogene, promoting myeloid and B-cell leukemic development (119). (D) Heterozygous loss of cohesin leads to changes in nuclear architecture that can alter enhancer-promoter interactions and lead to gene expression changes that promote myeloid transformation. Teaching point: There are many routes that enhancer perturbation can lead to cancer development.

 


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How to Cite

Puja Agrawal, Katelyn E. Heimbruch, Sridhar Rao. Genome‐Wide Maps of Transcription Regulatory Elements and Transcription Enhancers in Development and Disease. Compr Physiol 2018, 9: 439-455. doi: 10.1002/cphy.c180028