Nestled in the picturesque hillside of Heidelberg, Germany, the inaugural Principles of Chromosome Structure and Function meeting brought together biologists, biophysicists and biochemists at EMBL’s Advanced Training Center from September 5-8, 2018 to discuss their most recent breakthroughs in chromosome dynamics. The meeting was held just up the road from a ruined 16th century castle, a historic setting that mirrored the historic atmosphere of the meeting which brought together a diverse group of researchers to share their insights into chromosome function, particularly through the cell cycle.
The meeting began with its first of two keynote speakers, Dr. Edith Heard, who shared her recent work exploring the mechanisms that drive X chromosome inactivation in mammals. Work from her lab suggests that although the two chromosomes come physically close together during cellular development, this pairing is not necessary for the expression of factors that drive monoallelic inactivation. Instead, using carbon copy chromatin conformation capture (5C), they discovered that the pro-inactivation regulatory elements exist in one three-dimensional chromatin structure, or topologically associated domain (TAD), whereas anti-inactivation elements are clustered within another. Her group showed that fluctuations between compacted and elongated chromatin states change the interaction between the TADs and Xist, the primary driver of inactivation, and ultimately drive the inactivation of one chromosome over the other.
The remaining speakers on Wednesday’s program shared their insight on the relationship between TADs, gene expression, and the components that establish and maintain chromatin structures. Using evidence from yeast to mice, the speakers explored the function of the CTCF protein either between or within TAD boundaries, tracked the movement of chromosomes after a double-stranded break, and used advanced microscopy techniques to understand the structure of chromatin in both compacted and elongated states. Dr. Nick Gilbert introduced the concept of chromatin-associated RNAs that form a nuclear mesh with proteins to hold segments of active chromatin open while they’re being transcribed, and Dr. Wendy Bickmore showed that the nuclear pore is needed for normal heterochromatin organization.
On Thursday, the meeting opened with a talk by Dr. Mario Nicodemi that showed how modelling chromatin with polymer physics and machine learning can predict the location of important binding sites. The next session included experiments visualizing DNA molecules as they extruded to form loops, and an exciting presentation from Dr. Leonid Mirny showing how his group measured chromatin contacts across mitosis to develop a nested loop model for the structure of a metaphase chromosome. In the afternoon, Dr. Clodagh O’Shea shared her FIREnano technique to visualise the structure of chromatin during active states, and the remaining speakers presented their work pairing genetics with microscopy to visualize the changing structure of chromatin during mitosis, nuclear membrane formation and X inactivation.
Friday was all about chromosome structural proteins. The morning talks covered the role of condensin II and I in primary chromatin loops and nested loops by Dr. Bill Earnshaw. The afternoon focusing on the functions of cohesin in DNA supercoiling and gene transcription. Dr. John Marko gave a memorable presentation on the physical properties of a mitotic chromosome, where he compared a nucleus to a plastic bag filled with socks (with visual aids). Dr. Ana Cuadrado showed that the cohesin-SA1 complex is responsible for long range chromatin contacts whereas cohesin-S2 is involved in more local contacts in mouse embryonic stem cells.
The last day of the meeting showcased innovative advancements in technology, with Dr. Ana Pombo demonstrating the use of genome architecture mapping (GAM), which combines powerful microscopy in nuclear slices with more traditional ligation-based sequencing, to visualize chromatin architecture in relation to other nuclear structures in rare cell types. Dr. Elena Espinosa cleverly modified traditional Cre-Lox recombination to measure the duration of contact between sister chromatids in bacteria. Dr. Jelena Erceg used DNA paint to show that higher rates of gene expression occur between homologous chromosomes that are more tightly paired in Drosophila.
The second of the meeting’s keynote addresses was given by Dr. Job Dekker, the pioneer of chromatin conformation capture (3C) based techniques. He highlighted his recent work exploring the dynamics of chromosome folding, particularly as they pass through the cell cycle. He used long range contact maps to discover that there are two intermediate structural states during metaphase that correspond to an initial array of loops that then further condensed into nested loops; this had been predicted by others at the meeting. His group has also developed a novel technique to measure the attraction between similar chromatin compartments in the interphase nucleus and has conducted time course experiments to measure the kinetics and stability of these interactions over time.
The idea that chromatin is arranged in functional units within the nucleus was proposed over 100 years ago, but it has only been within the last two decades that scientists have had the technology to begin to examine the dynamics and functional implications of chromosome structure. The enthusiasm of all the participants at this year’s meeting, either during the poster sessions or coffee breaks, speaks to the explosion of technological and scientific advancements that will continue to come from the field as we prepare for the next Principles of Chromatin Structure and Function conference in 2020.
Special thanks to Kathryn Vaillancourt for providing this sumary