Genome Decompaction By Condensin Depletion In S. Cerevisiae

The research article “Condensin Depletion Causes Genome Decompaction Without Altering the Level of Global Gene Expression in Saccharomyces cerevisiae” by Matthew Robert Paul, Tovah Elise Markowitz, Andreas Hochwagen, and Sevinc Ercan, a scientific journal, examined the role that condensin depletion may play in genome decompaction and investigated if this interaction affected global gene expression. The purpose of this paper was to study condensin to analyze genome decompaction and global gene expression. There was no evidence found that lack of condensin can cause a global change of gene expression, but it was found that condensin affects gene interactions.

The first experiment looked into the connection between chromosome structure and the expression and mutation of genes using 3-seq analysis. In the nuclei of the yeast cells, the condensin was removed by targeting a subunit and using rapamycin. Cells that were not tagged with this subunit were used as a control. Nuclei that got the treatment were shown to have two mutations at amino acids 219 and 225, which is otherwise known as ycs4-2 mutation. Furthermore, there was also temperature-activated mutant that had inactive condensin at 37°C for this study. The second experiment focused on the interactions between different part of the loci on the chromosome using distance decay curves. From this, it was determined that cis-interactions were more common than trans-interactions.

Distance decay curves were also used to measure cis-interaction and it was determined that these interactions are more likely to occur with decreasing distance between the loci. In the ycs4-2 mutants, there were less interactions with loci that were in close proximity, but there were more trans and long-distance cis-interactions. The next experiment used heat mapping to see if condensin removal could affect centromeres during metaphase. The heat maps contained many non-random trans-interactions so it was found that condensin depletion did not affect the ability of the centromere to bind to the spindle pole or affect telomere clustering in cycling cells.

It is suspected that condensin does help contribute to the Rab1 conformation of chromosome arms. The loss of condensin caused less interactions between the two arms of the chromosome, which is different from the wild-type. It is suspected that condensin is needed to strengthen this Rab1 conformation of chromatin. Using cytological analyses, researchers were unable to determine a significant association between tRNA genes and rDNA. The study discovered that intrachromosomal interactions between two tRNA strands decreased when condensin was deleted and that eight of forty gene families relied partially on condensin, which means tRNA gene clustering could be impacted by condensin.

The condensin subunit was tagged and analyzed but did not support a relationship between condensin and clustering, but there are less interactions in regions that more condensin binding regions. RNA Polymerase III binding data was analyzed and it was determined that there was no relationship between polymerase III and condensin, but some tRNA genes that rely on condensin did have more polymerase III binding which could mean that clustering could promote more polymerase III binding. The tRNA genes near the replication origin were also analyzed and clustering was not affected by lack of condensin. Condesin depletion did not change clustering in the largest tRNA gene family of yeast.

From these analyses, it was determined that some tRNA genes, atleast one tRNA gene family, are dependent on condensin for clustering. An in silico 4C analysis was used to investigate if the effect of condensin is asymmetric because of polar interactions of the rDNA array flanks. This study used a control where CEN12 interaction was disrupted compared to typical interaction and found that rDNA only interacts with the centromere located on the same chromosome. It was found through analysis that there was more condensin between rDNA and CEN12 cells, which means the area between CEN12 and rDNA had more condensin-dependent binding and interactions. A mRNA-seq was conducted to investigate condensin inactivation, which found that the overall global gene expression was not changed after condensin was diminished. The yes4-2 and ycg1-2 mutants were also tested at the permissive and restrictive temperatures and both results indicate that these mutants had higher gene expression as compared to the wild-type. This means that the mutants are not effective at the permissive temperature. The yes4-2 mutant did not have any changes due to condensin which was different than yes4-2 which had an upregulation of genes on chromosome 12. It is suspected that the yes4-2 strain attempted to make up for the lack of condensin. From this study, one could learn more about the effect that condensin has on gene interactions and tRNA clusters and its lack of effect on global gene expression. One can also learn about different types of methods such as the 3-seq analysis, distance decay curves, heat mapping, and cytological analyses.

This paper is very through on its investigating on the role and effect of condensin but there is still more to learn particularly the regulation of loop extrusion and its relation to condensin regulating the cell cycle as well as how transcription may not rely on global chromosome structure for expression. This paper was well-written because it was easy to understand, and the figures supported the claims made in the paper. This study is effective because there were different types of methods involved for investigating the hypothesis including wild-type controls and research from other sources. Overall, this paper does contribute to science and has findings that might lead to future discoveries.