Dissecting the fundamentals of transcriptional regulation

Aïsha​ ​Mientjes



Seminar 7:​    

Speaker:​ ​Martin Howard

Department:​ John Innes Center

Subject:​ Dissecting the fundamentals of transcriptional regulation

Location:​ ​TU​ ​Delft

Date:​ 12-01-2018


On the 12th of January, there was a bionanoscience seminar given by Martin Howard. He was trained as a physicist, but he has since then moved into the field of biology as currently does research on epigenetic memory.

The presentation was started of by the question: when is transcription regulated in an on/off manner and when is it regulated in a continuous manner? In addition he asked whether the process is noisy/bursty or not. The rest of the seminar mainly concerned itself with the first question, because there was too little time to go into the second question.

Epigenetic inheritance means the inheritance of phenotype not based on the DNA sequence. Martin Howard studies epigenetics by zooming in on one locus. The system that he studies is called Arabidopsis, in particular flowering locus C (FLC). This locus is involved with aligning plant development with the seasons. The switch to flowering in a plant is repressed by FLC. FLC is in turn repressed by vernalization.


The level of FLC throughout the year.


Correct timing is very important for the FLC is very important because plants cannot flower too early or too late. In the graph above it is visible that the level of expression on return to the warm period depends on the length of the cold period. The Arabidopsis model is very slow, which can be difficult in experiments but also allows a very quantitative study.


After an explanation of the model, the speaker went on to explain about epigenetic memory. This memory can be stored in a trans way and in a cis way. Trans means that it is stored in diffusible factors and is uniformly distributed, cis means that it is stored in chromatin based histone modifications and is locally stored. There is still an active debate in biology as to how the memory is stored.


Systems for digital cell autonomous epigenetic memory is bi-stable. For an individual cell, it is all or nothing. With this knowledge, it can be concluded that the quantitative quality (shown in the graph above) must come from the fraction of cells. The final part of the presentation concerned an experiment with which Martin Howard showed that there is a favour for the cis memory.


I found this seminar very interesting because it largely concerned ecology, a subject which is not often discussed during these seminars. I found the model quite interesting and it was nice to hear that a lot of field research was done for the discussed experiments as well. The final part of the presentation was quite difficult to understand but the rest was fairly easy to follow in my opinion. In addition, I liked that Martin Howard has a very ‘physicist’ way to explore biology, he focussed on a single locus which made it quite easy to explain epigenetics.


Targeting Epigenetic Changes in Immune Cells: Implications in Disease

Speaker: Esteban Ballestar
Department: Bellvitge Medical Research Institute (IDIBELL), Barcelona Spain
Location: Erasmus MC
Date: July 13, 2017
Author: Teun Huijben

Esteban Ballestar got his Bachelor and Master degree at the University of Valencia in Spain, followed by a PhD. Afterwards he did a Postdoc abroad and returned to start his own research group at the same university. The main interest of his group is the DNA methylation, and especially in the context of diseases involving the immune system.

The first part of Estebans talk was about mapping DNA methylation in immunological diseases to understand which proteins are involved in the disease. The group of diseases they studied were Common Variable Immunodeficiencies Diseases (CVID) in which the body has not enough primary antibodies. These diseases are mostly caused by severe deficiencies in the number of switched memory B-cells. With switched B-cells we mean activated B-cells that start producing the antibodies in high quantities after recognizing the antigen. By mapping the DNA methylations of these B-cells, they hope to find genes that are differently methylated and are mostly likely causing the disease.

Methylation of DNA means that a methyl group is added to the 5-prime end of a cytosine (5mC) nucleobase. This can only be done if the cytosine is next to a guanine (see Figure 1). DNA methylation is maintained by de-novo DNA methyltransferases (mostly DNMT1, DNMT3A and DNMT3B). DNA methylations can be actively removed by demethylation, in which the 5mC is oxidized to a 5hmC or 5caC. Adding or removing methyl group to the DNA has an effect on the gene expression of that particular gene.


Figure 1: DNA methylation. The cytosine of the CG-pair gets methylated by a de-novo methyltransferase (DNMT). [S. Zakhari 2015]

To identify disease causing genes, Estebans group did DNA methylation profiling of the B-cells from a CVID patient. To eliminate as much side effects as possible, thy only investigated twins of which one sibling had CVID and the other was healthy. After collecting the B-cells, they performed DNA methylation profiling and looked at genes with different methylation profiles between the two brothers. They found 230 genes that are more methylated in the CVID patient and 81 genes that are less methylated. Gene ontology analysis showed that most of the genes were related to immune responses, indicating that changing the gene expression of these genes can cause an immune related disease.

All the genes that showed different methylation profiles between healthy and CVID patient, were taken into further research. The B-cells are sorted on the fact whether they were naive (not yet switched to active) or switched. They found that in healthy persons most genes got demethylated after the transformation from naive to switched. On the other hands, the same genes in CVID patients showed no decrease in methylation, a second indication that these genes are involved in the disease.

However, the question remains whether the different methylation profile itself causes the disease, or is it a downstream effect caused by other factors. To investigate this, more research needs to be done on this subject. Also, more methylation profiles of twins are needed to draw real conclusions about the disease causing genes, since one set of results of the statistically valid enough. Overall, the talk of Esteban was interesting and he is a very good speaker. Despite using many difficult immunology term, he explained very clear the research his lab is doing.