Enhancer regulation of transcriptional bursting parameters revealed by forced chromatin looping

By Caroline Bartman, Sarah Hsu, Chris Hsiung, Arjun Raj, Gerd Blobel

Link to Manscript


Questions: all,

The data presented at the beginning is in a mouse erythroblast line called G1E.  These cells can be induced to differentiate by addition of estradiol, which stabilizes a GATA1-estrogen-receptor fusion expressed by these cells. GATA-1 is the master transcription factor of erythroid cells and goes on to cause transcription of globin and other important erythroid genes. (These slides are tagged with a mouse icon.)

The later data is in human erythroid cells, which were differentiated in vitro from human CD34+ pluripotent cells isolated from human blood. These cells are differentiated by changing their media to a pro-differentiation media including the cytokine erythropoietin. (These slides are tagged with a human icon.)

Patients with sickle cell disease or beta-thalassemia produce mutant adult beta-globin or no adult beta-globin, respectively. If we are able to therapeutically induce such patients to transcribe fetal beta-globin, this can ameliorate their symptoms.

Golding, I., Paulsson, J., Zawilski, S.M., and Cox, E.C. (2005). Real-time ki- netics of gene activity in individual bacteria. Cell 123, 1025–1036.

Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y., and Tyagi, S. (2006). Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309–e313.

Molina, N., Suter, D.M., Cannavo, R., Zoller, B., Gotic, I., and Naef, F. (2013). Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proc. Natl. Acad. Sci. USA 110, 20563–20568.

This paper (reference shown below) used an artificially constructed locus in Drosophila in which two promoters were controlled by the same enhancer which was placed centrally, between the two genes. Using MS2/PP7 technology, the transcription of these two genes could be visualized by live imaging. Their findings were consistent with ours in showing that enhancer looping controls burst fraction without affecting burst size. They also found some evidence for promoter competition as we did, however they also observed that the two genes transcribed by the same enhancer could fire in tandem by live imaging. 

Generally the conclusions of the two papers are quite consistent; the main differences are in cell and gene systems and imaging methodologies employed.



Enhancer Control of Transcriptional Bursting.

Fukaya T, Lim B, Levine M.

Cell. 2016 Jul 14;166(2):358-68. doi: 10.1016/j.cell.2016.05.025.


Femino, A.M., Fay, F.S., Fogarty, K., and Singer, R.H. (1998). Visualization of single RNA transcripts in situ. Science 280, 585–590.

Raj, A., van den Bogaard, P., Rifkin, S.A., van Oudenaarden, A., and Tyagi, S. (2008). Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877–879.