Chromosome Tethering in Yeast

On July 14, 2014, PLOS ONE  published a paper from the Haber and Kondev labs. The paper, Effect of chromosome tethering on nuclear organization in yeast, was authored by Baris Avsaroglu, Gabriel Bronk, Susannah Gordon-Messer, Jungoh Ham, Debra A. Bressan, James E. Haber, and Jane Kondev.

by Baris Avsaroglu

Chromosopone.0102474_350mes are folded into the cell nucleus in a non-random fashion. In yeast cells the Rabl model is used to describe the folded state of interphase chromosomes in terms of tethering interactions of the centromeres and the telomeres with the nuclear periphery. By combining theory and experiments, we assess the importance of chromosome tethering in determining the spatial location of genes within the interphase yeast nucleus. Using a well-established polymer model of yeast chromosomes to compute the spatial distributions of several genetic loci, we demonstrate that telomere tethering strongly affects the positioning of genes within the first 10 kb of the telomere. Further increasing the distance of the gene from the telomere reduces the effect of the attachment at the nuclear envelope exponentially fast with a characteristic distance of 20 kb. We test these predictions experimentally using fluorescently labeled genetic loci on chromosome III in wild type and in two mutant yeast strains with altered tethering interactions. For all the cases examined we find good agreement between theory and experiment. This study provides a quantitative test of the polymer model of yeast chromosomes, which can be used to predict long-ranged interactions between genetic loci relevant in transcription regulation and DNA recombination.

How regulatory sequences evolve in fruit flies

An IMP-Brandeis collaboration reveals the evolution of regulatory sequences in Drosophilids

By Yuliya Sytnikova and Nelson Lau

Enhancers are cis-regulatory DNA sequences that influence the promoters of genes, but identifying enhancers is not a straightforward process. Previously, the Stark lab developed a method for genome-wide enhancer detection called STARR-seq, (Arnold, Gerlach et al. 2013), that allowed them to identify thousands of enhancer sequences around the Drosophila melanogaster genome. In the most recent issue of Nature Genetics, a collaboration between the Stark lab of the IMP (Institute of Molecular Pathology) in Vienna, Austria, and the Lau lab at Brandeis University examines this hypothesis by studying the conservation of enhancer regulatory regions during Drosophilid fly evolution.

To ask if enhancers from D. melanogaster enhancers are also conserved in other Drosophila species in their sequences and locations, the Stark lab extended the STARR-Seq approach to D.yakuba and D.ananassae, which are separated from D.melanogaster by 11 and 40 million years ago, respectively (Arnold, Gerlach et al. 2014). Interestingly, this study also revealed hundreds of new sequences that gained enhancer function differentially between D.yakuba, D.ananassae, and D.melanogaster.

However, to test if these new sequences meaningfully direct different gene expression changes, the Lau lab conducted a targeted mRNA profiling experiment in purified endogenous follicle cells from D.yakuba and D.ananassae. The Stark lab had initiated the STARR-Seq analysis in an Ovarian Somatic Cell (OSC) line, which originated from the follicle cells of D.melanogaster, therefore the profiling of endogenous follicle cells from D.yakuba and D.ananassae was critical. The Lau lab achieved this using a methodology they developed for profiling Piwi-interacting RNAs from these cells (Matts, Synikova et al. 2013).

Figure 6: Evolution of enhancer activity in OSCs and gene expression in follicle cells in vivo.


Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. Nat Genet. 2014 Jun 8. doi: 10.1038/ng.3009. [Epub ahead of print] Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution.

Matts JA, Sytnikova Y, Chirn GW, Igloi GL, Lau NC. Methods Mol Biol. 2014;1093:123-36. doi: 10.1007/978-1-62703-694-8_10. Small RNA library construction from minute biological samples.


Eapen wins HHMI International Student Research Fellowship

Vinay Eapen from the Haber Lab in Biology has been awarded an HHMI International Student Research Fellowship. These fellowships, highly sought-after, are among the few available to international students studying at major research universities in the US – there were only 42 recipients nationwide. Eapen is a graduate student entering his fourth year in the Molecular and Cell Biology PhD program at Brandeis, and already has 4 publications from Brandeis to his credit resulting from his studies of the DNA damage checkpoint and autophagy in yeast.


Med School and Grad School in the Lone Star State

Wensink lab alum Mien-Chie Hung (PhD ’84), who is currently Ruth Legett Jones Distinguished Chair at  The University of Texas MD Anderson Cancer Center, will give seminar on Monday, Dec 3 at noon in Rosenstiel 118 on “Novel signaling pathways in cancer cells and their crosstalk to predict resistance for target therapy“.  He will also meet with interested students on Monday Dec. 3 in the Alumni Lounge in Usdan at 7 PM; there will be pizza.   He will talk with undergrads, prospective grad and med students about medical schools and graduate schools in Texas Medical Center including MD Anderson, UT Health Science Center and Baylor.

It’s not all transcription! New insights on how biological rhythms are generated

Sleepy during the day? Hungry at night? You should check your biological clock!

As in every organism, humans are exposed to daily variations of their environment. There is obviously the day/night cycle, but significant variations of temperature and humidity also occur in temperate regions of the globe. To survive to these environmental changes, organisms have evolved so that their biology, biochemistry, physiology and behavior are rhythmically regulated on a 24hr-basis. Humans are no exception, and most (if not all) of our biological functions are set to function optimally at the most appropriate time of the day. For example, the physiology of muscle cells is rhythmic so that their capacity of coping with physical activity is maximal during the day.

A lot of progress has been made over the last two decades to uncover the molecular underpinnings of circadian (for circa, about and dies, day) rhythms. To keep the story short, in all eukaryotes the circadian system relies on transcriptional feedback loops that operate at the level of individual cells (see figure 1). In mammals, these loops are composed of the two transcription factors CLK and BMAL1, which act as a heterodimeric complex to activate the expression of the transcriptional repressors Period (Per1, Per2 and Per3) and Cryptochrome (Cry1 and Cry2). When expressed, these repressor proteins are post-translationally modified (e.g., phosphorylation) and feedback to inhibit the transcriptional activity of CLK:BMAL1. As a result, transcription of Per and Cry genes is shut-off. The progressive degradation of the PER and CRY proteins then leads to a new cycle of CLK:BMAL1-mediated transcription. Importantly, these transcriptional oscillations regulate the rhythmic expression of a large fraction of the transcriptome (up to 10-15% of all mRNAs). These output genes, also called “clock-controlled genes”, are rhythmically regulated in a tissue-specific manner, and are responsible for the daily oscillations of biological functions.

As in other biological systems, it is generally assumed that daily variations of mRNA levels are a direct consequence of transcription regulation. However, there is growing evidence that post-transcriptional events such as mRNA splicing, polyadenylation, nuclear export and half-life also contribute to changes in the amount of mRNA expressed by particular genes. Such post-transcriptional processes are known to have a role in other areas of cell biology but until very recently this had not been studied in detail at a genome-wide level.

This is the question addressed by Jerome Menet, Joseph Rodriguez, Katharine Abruzzi and Michael Rosbash, in a paper recently published at eLife (Menet et al., 2012). The authors directly assayed rhythmic transcription by measuring the amount of nascent RNA being produced at a given time, six times a day, across all the genes in mouse liver cells using a high-throughput sequencing approach called Nascent-Seq (see figure 2). They compared this with the amount of liver mRNA expressed at six time points of the day. Although the authors found that many genes exhibit rhythmic mRNA expression in the mouse liver, about 70% of them did not show comparable transcriptional rhythms. Post-transcriptional regulations have therefore a major role in the circadian system of mice. Interestingly, similar experiments performed by Joe Rodriguez in the Rosbash lab using Drosophila as the model system led to the same conclusions, suggesting that the contribution of post-transcriptional events to the generation of circadian rhythms is common to all animals (Rodriguez et al., in press).

To assess the contribution of the core molecular clock to genome-wide transcriptional rhythms, Menet et al. also examined how rhythmic CLK:BMAL1 DNA binding directly affects the transcription of its target genes. They found that although maximal binding occurs at an apparently uniform phase, the peak transcriptional phases of CLK:BMAL1 target genes are heterogeneous, which indicates a disconnect between CLK:BMAL1 DNA binding and its transcriptional output.

The data taken together reveal novel regulatory features of rhythmic gene expression and illustrate the potential of Nascent-Seq as a genome-wide assay technique for exploring a range of questions related to gene expression and gene regulation.

Menet JS, Rodriguez J, Abruzzi KC, Rosbash M. Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation. elife. 2012;1:e00011. doi: 10.7554/eLife.00011.

Rodriguez J, Tang CHA, Khodor YL, Vodala S, Menet JS, Rosbash M. Post-transcriptional events regulate genome-wide rhythmic gene expression in Drosophila. Proc Natl Acad Sci U S A. (In press).

Looking for Fun(30)

A recent paper from the Haber lab by Eapen et al., “The Saccharomyces cerevisiae Chromatin Remodeler Fun30 Regulates DNA End Resection and Checkpoint Deactivation“, is the most read paper from the journal Molecular and Cell Biology for October 2012. Join the fun, read the paper!

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