The last few years have provided us with a new level of understanding of how chromosomes are replicated, segregated and read - and how their 3D organisation influences expression of individual genes (and vice versa). The rapid pace of development in the field is reflected by the first dedicated meeting on chromosome biology in the EMBO-EMBL Symposium series in Heidelberg. For those who are unable to attend the meeting, or just want more background reading on the topics covered, we have created the following collection of recent papers published in EMBO reports, Molecular Systems Biology and The EMBO Journal. We hope you will enjoy them!
Featured Articles
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The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion MP Ivanov, R Ladurner, I Poser, R Beveridge, E Rampler, O Hudecz, M Novatchkova, J-K Hériché, G Wutz, P van der Lelij, E Kreidl, JRA Hutchins, H Axelsson-Ekker, J Ellenberg, AA Hyman, K Mechtler, J-M Peters Recruitment of cohesin acetyltransferase ESCO2 by the MCM2-7 replication complex to chromatin is required for cohesin acetylation around replication forks to maintain centromeric cohesion. The EMBO Journal (2018) 37, e97150 DOI 10.15252/embj.201797150 |
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Forces driving the three‐dimensional folding of eukaryotic genomes A Rada‐Iglesias, FG Grosveld, A Papantonis This review discusses recent work highlighting biophysical and regulatory forces contributing to higher‐order genome organization and proposes that chromatin conformations are not so much the result of a linear hierarchy, but rather of both converging and conflicting dynamic forces. Molecular Systems Biology 14, e8214 DOI 10.15252/msb.20188214 |
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Cohesin: building loops, but not compartments JHI Haarhuis, BD Rowland Recent work demonstrates that cohesin loading is essential for the 3D organization of vertebrate genomes via active loop extrusion. The EMBO Journal (2017) 36, 3549-3551 DOI 10.15252/embj.201798654 |
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HP1 links centromeric heterochromatin to centromere cohesion in mammals Q Yi, Q Chen, C Liang, H Yan, Z Zhang, X Xiang, M Zhang, F Qi, L Zhou, F Wang Sister-chromatid cohesion must be properly regulated to prevent chromosome mis-segregation and chromosomal instability. HP1 proteins bind to the cohesin protector Haspin and promote its centromeric localization, thereby protecting cohesion at mitotic centromeres. EMBO Reports (2018) 19: e45484 DOI 10.15252/embr.201745484 |
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Real-time detection of condensing-driven DNA compaction reveals a multistep binding mechanism JM Eeftens, S Bisht, J Kerssemakers, M Kschonsak, CH Haering, C Dekker Single-molecule experiments suggest that condensin contacts DNA via electrostatic interactions before ATP hydrolysis, resulting in topological entrapment and compaction of DNA. The EMBO Journal (2017) 36: 3448–3457 DOI 10.15252/embj.201797596 |
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Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C H Muller, VF Scolari, N Agier, A Piazza, A Thierry, G Mercy, S Descorps‐Declere, L Lazar‐Stefanita, O Espeli, B Llorente, G Fischer, J Mozziconacci, R Koszul A 144‐kb region of a yeast chromosome is engineered to display regularly spaced restriction sites to ultimately track homolog pairing during meiotic prophase. The engineered chromosome region (Syn‐HiC) displays a smoother Hi‐C signal at restriction fragment resolution. Molecular Systems Biology 14, e8293 DOI 10.15252/msb.20188293 |
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HP1α targets the chromosomal passenger complex for activation at heterochromatin before mitotic entry JG Ruppert, K Samejima, M Platani, O Molina, H Kimura, AA Jeyaprakash, S Ohta, WC Earnshaw Tethering experiments and detection of H3S10 phosphorylation in G2 suggest that HP1 initially clusters the chromosomal passenger complex for activation, before other epigenetic marks determine its cent localisation in mitosis. The EMBO Journal (2018) 37: e97677 DOI 10.15252/embj.201797677 |
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RNA polymerase II primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation C Ferrai, E Torlai Triglia, JR Risner‐Janiczek, T Rito, OJL Rackham, I de Santiago, A Kukalev, M Nicodemi, A Akalin, M Li, MA Ungless, A Pombo Poised RNAPII‐S5p is present at Polycomb‐repressed genes from embryonic stem cells to terminally differentiated neurons. The tight interplay between RNAPII poising and Polycomb repression enables promoter plasticity in differentiated cells and increased potential for reactivation. Molecular Systems Biology (2017) 13, 946 DOI 10.15252/msb.20177754 |
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Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks S Hiraga, C Monerawela, Y Katou, S Shaw, KRM Clark, K Shirahige, AD Donaldson This study identifies genome‐wide Rif1 bindings sites in budding yeast. Rif1 binds both replication origins and stalled replication forks and protects nascent DNA from degradation. EMBO Reports (2018) e46222 DOI 10.15252/embr.201846222 |
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Chromosome structure dynamics during the cell cycle: a structure to fit every phase C Barrington, D Pezic, S Hadjur Recent H-C studies provide a comprehensive view of chromosome dynamics throughout the cell cycle, highlighting stage-specific genome structure and the orchestrating role played by SMC complexes. The EMBO Journal (2017) 36, 2661-2663 DOI 10.15252/embj.201798014 |
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KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control CHC Tie, L Fernandes, L Conde, L Robbez‐Masson, RP Sumner, T Peacock, MT Rodriguez‐Plata, G Mickute, R Gifford, GJ Towers, J Herrero, HM Rowe KAP1 represses ERVs during development by interacting with their repetitive sequences through KRAB‐zinc finger proteins. KAP1 regulation of ERVs persists in adult human cells, which promotes genome stability and reduces autoimmune responses. EMBO reports (2018) e45000 DOI 10.15252/embr.201745000 |
FURTHER READING
The EMBO Journal
| Histone H2A-H2B binding by Pol α in the eukaryotic replisome contributes to the maintenance of repressive chromatin C Evrin, JD Maman, A Diamante, L Pellegrini, K Labib The EMBO Journal (2018) e99021 DOI 10.15252/embj.201899021 |
| Rtt105 functions as a chaperone for replication protein A to preserve genome stability S Li, Z Xu, J Xu, L Zuo, C Yu, P Zheng, H Gan, X Wang, L Li, S Sharma, A Chabes, D Li, S Wang, S Zheng, J Li, X Chen, Y Sun, D Xu, J Han, K Chan, Z Qi, J Feng, Q Li The EMBO Journal (2018) e99154 DOI 10.15252/embj.201899154 |
| Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome PG Maass, A Weise, K Rittscher, J Lichtenwald, AR Barutcu, T Liehr, A Aydin, Y Wefeld-Neuenfeld, L Pölsler, S Tinschert, JL Rinn, FC Luft, S Bähring The EMBO Journal (2018) 37: e96257 DOI 10.15252/embj.201796257 |
| Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins G Wutz, C Várnai, K Nagasaka, DA Cisneros, RR Stocsits, W Tang, S Schoenfelder, G Jessberger, M Muhar, MJ Hossain, N Walther, B Koch, M Kueblbeck, J Ellenberg, J Zuber, P Fraser, J-M Peters The EMBO Journal (2017) 36: 3573–3599 DOI 10.15252/embj.201798004 |
| A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture J Gassler, HB Brandão, M Imakaev, IM Flyamer, S Ladstätter, WA Bickmore, J-M Peters, LA Mirny, K Tachibana The EMBO Journal (2017) 36: 3600–3618 DOI 10.15252/embj.201798083 |
Molecular Systems Biology
| Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models Lin Yang, Yaron Orenstein, Arttu Jolma, Yimeng Yin, Jussi Taipale, Ron Shamir, Remo Rohs Molecular Systems Biology (2017) 13, 910 DOI 10.15252/msb.20167238 |
| A unified approach for quantifying and interpreting DNA shape readout by transcription factors H Tomas Rube, Chaitanya Rastogi, Judith F Kribelbauer, Harmen J Bussemaker Molecular Systems Biology 14, e7902 DOI 10.15252/msb.20177902 |
| Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics Thomas Brown, Françoise S Howe, Struan C Murray, Meredith Wouters, Philipp Lorenz, Andrew Angel, Jane Mellor Molecular Systems Biology 14, e8007 DOI 10.15252/msb.20178007 |
EMBO reports
| Mechanisms for stalled replication fork stabilization: new targets for synthetic lethality strategies in cancer treatments Hongwei Liao, Fang Ji, Thomas Helleday, Songmin Ying EMBO reports (2018) e46263 DOI 10.15252/embr.201846263 |
| DNA damage-induced replication stress results in PA200-proteasome-mediated degradation of acetylated histones Imke K Mandemaker, Marit E Geijer, Iris Kik, Karel Bezstarosti, Erikjan Rijkers, Anja Raams, Roel C Janssens, Hannes Lans, Jan HJ Hoeijmakers, Jeroen AA Demmers, Wim Vermeulen, Jurgen A Marteijn EMBO reports (2018) e45566 DOI:10.15252/embr.201745566 |
| The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization Pedro Prudêncio, Leonardo G Guilgur, João Sobral, Jörg D Becker, Rui Gonçalo Martinho, Paulo Navarro‐Costa EMBO reports (2018) 19, e45728 DOI 10.15252/embr.201845728 |
| Tel1/ATM prevents degradation of replication forks that reverse after topoisomerase poisoning Luca Menin, Sebastian Ursich, Camilla Trovesi, Ralph Zellweger, Massimo Lopes, Maria Pia Longhese, Michela Clerici EMBO reports (2018) 19, e45535 DOI 10.15252/embr.201745535 |
| RNase H eliminates R-loops that disrupt DNA replication but is nonessential for efficient DSB repair Hongchang Zhao, Min Zhu, Oliver Limbo, Paul Russell EMBO reports (2018) 19, e45335 DOI 10.15252/embr.201745335 |
