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Chromosome Structure and Function (2018)


 

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

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
 
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
 
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
 
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
 
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
 
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


 
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
 
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
 
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
 
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
 
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
 

In this Issue
Volume 15, Issue 2
01 February 2019
Molecular Systems Biology: 15 (2)
About the cover

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