Chromatin, Epigenetics, Genomics & Functional Genomics
- Loss of pollen‐specific phospholipase NOT LIKE DAD triggers gynogenesis in maize
- Laurine M Gilles1,2,
- Abdelsabour Khaled1,3,
- Jean‐Baptiste Laffaire2,
- Sandrine Chaignon1,
- Ghislaine Gendrot1,
- Jérôme Laplaige1,
- Hélène Bergès4,
- Genséric Beydon4,
- Vincent Bayle1,
- Pierre Barret5,
- Jordi Comadran2,
- Jean‐Pierre Martinant2,
- Peter M Rogowsky1 and
- Thomas Widiez (thomas.widiez{at}ens-lyon.fr)*,1
- 1Laboratoire Reproduction et Développement des Plantes, Univ Lyon ENS de Lyon UCB Lyon 1 CNRS, INRA, Lyon, France
- 2Limagrain Europe SAS, Research Centre, Chappes, France
- 3Department of Genetics, Faculty of Agriculture, Sohag University, Sohag, Egypt
- 4INRA, US1258 Centre National des Ressources Génomiques Végétales, Auzeville, France
- 5INRA, UMR1095 Génétique, Diversité, Ecophysiologie des Céréales, Clermont‐Ferrand, France
- ↵*Corresponding author. Tel: +33 4 72 72 86 08; E‐mail: thomas.widiez{at}ens-lyon.fr
The function of the patatin‐like phospholipase A NOT LIKE DAD (NLD) in the sperm cells of maize pollen is necessary for successful fertilization, whereas its disruption promotes the development of haploid embryos, which represent an important plant breeding tool.
Synopsis
The function of the patatin‐like phospholipase A NOT LIKE DAD (NLD) in the sperm cells of maize pollen is necessary for successful fertilization, whereas its disruption promotes the development of haploid embryos, which represent an important plant breeding tool.
Fine mapping restricted a major QTL (quantitative trait locus) responsible for haploid induction in maize to an interval containing a single gene coding for NLD.
A 4‐bp insertion in NLD leading to a predicted truncated protein is responsible for haploid induction.
Expression of NLD is restricted to sperm cells.
Wild‐type NLD is anchored to the plasma membrane, whereas the truncated protein present in inducer lines loses its membrane attachment.
Mutation of NLD orthologs may allow to establish doubled haploid breeding techniques in crop species lacking such tools.
The EMBO Journal (2017) 36: 707–717
- Received January 26, 2017.
- Revision received February 8, 2017.
- Accepted February 9, 2017.
- © 2017 The Authors
- Molecular role of the PAX5‐ETV6 oncoprotein in promoting B‐cell acute lymphoblastic leukemia
- Leonie Smeenk1,6,
- Maria Fischer1,
- Sabine Jurado1,
- Markus Jaritz1,
- Anna Azaryan1,
- Barbara Werner1,
- Mareike Roth1,
- Johannes Zuber1,
- Martin Stanulla2,
- Monique L den Boer3,
- Charles G Mullighan4,
- Sabine Strehl5 and
- Meinrad Busslinger (busslinger{at}imp.ac.at)*,1
- 1Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- 2Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
- 3Department of Pediatric Oncology and Hematology, Erasmus Medical Center, Sophia Children Hospital, Rotterdam, The Netherlands
- 4Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
- 5Children's Cancer Research Institute, St. Anna Kinderkrebsforschung e.V., Vienna, Austria
- 6Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- ↵*Corresponding author. Tel: +43 1 79730 3150; Fax: +43 1 79730 223150; E‐mail: busslinger{at}imp.ac.at
New mouse models for PAX5 fusion proteins found in acute lymphoblastic leukemia reveal that oncogenesis involves loss of cell cycle inhibitors rather than deregulation of known PAX5 target genes.
Synopsis
New mouse models for PAX5 fusion proteins found in acute lymphoblastic leukemia reveal that oncogenesis involves loss of cell cycle inhibitors rather than deregulation of known PAX5 target genes.
Expression of the Pax5‐Etv6 fusion protein (as generated by recurrent translocations in human B‐ALLs) arrests B‐cell development at the pre‐BCR+ stage in a Pax5Etv6/+ mouse model.
Pax5‐Etv6 functions as a potent oncoprotein that cooperates with loss of the tumor suppressor proteins Cdkn2a and Cdkn2b in the development of B‐cell acute lymphoblastic leukemia (B‐ALL).
Pax5‐Etv6 regulates genes involved in cell adhesion and migration, which explains the broad tissue infiltration of Pax5Etv6/+ Cdkn2ab+/− B‐ALLs.
The likely cell of origin for B‐ALL development is the pre‐BCR+ B cell, consistent with the Pax5‐Etv6‐dependent regulation of key genes involved in pre‐BCR signaling.
The EMBO Journal (2017) 36: 718–735
- Received August 14, 2016.
- Revision received January 9, 2017.
- Accepted January 10, 2017.
- © 2017 The Authors
- PRC2 is dispensable for HOTAIR‐mediated transcriptional repression
- Manuela Portoso1,2,
- Roberta Ragazzini1,2,
- Živa Brenčič1,2,
- Arianna Moiani1,2,
- Audrey Michaud1,2,
- Ivaylo Vassilev1,2,
- Michel Wassef1,2,
- Nicolas Servant1,3,
- Bruno Sargueil4 and
- Raphaël Margueron (raphael.margueron{at}curie.fr)*,1,2
- 1Institut Curie, PSL Research University, Paris, France
- 2INSERM U934, CNRS UMR3215, Paris, France
- 3INSERM U900, Mines ParisTech, Paris, France
- 4CNRS UMR 8015, Université Paris Descartes, Paris, France
- ↵*Corresponding author. Tel: +33 156246551; Fax: +33 156246939; E‐mail: raphael.margueron{at}curie.fr
Recruitment of chromatin‐modifying factors may not be the sought‐after mechanism for gene silencing by HOTAIR lncRNA, but rather its downstream consequence.
Synopsis
The ability of lncRNA HOTAIR to recruit chromatin‐modifying factors has served as a paradigm for lncRNA‐mediated repression of target genes. Contrary to expectation, HOTAIR can exert repressive effects independent of PRC2, whose recruitment may rather be a downstream consequence of gene silencing.
Overexpression of lncRNA HOTAIR in breast cancer cells has limited transcriptional consequences.
Artificial tethering of HOTAIR at a reporter transgene leads to transcriptional repression.
The transcriptional repression mediated by HOTAIR is independent of PRC2.
The EMBO Journal (2017) 36: 981–994
- Received July 25, 2016.
- Revision received December 23, 2016.
- Accepted January 5, 2017.
- © 2017 Institut Curie. Published under the terms of the CC BY NC ND 4.0 license
This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs 4.0 License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
- Gene‐body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis
- Soichi Inagaki (soinagak{at}nig.ac.jp)*,1,2,
- Mayumi Takahashi1,
- Aoi Hosaka1,2,
- Tasuku Ito1,3,
- Atsushi Toyoda1,
- Asao Fujiyama1,
- Yoshiaki Tarutani1,2 and
- Tetsuji Kakutani (tkakutan{at}nig.ac.jp)*,1,2,3
- 1National Institute of Genetics, Mishima, Shizuoka, Japan
- 2Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
- 3Faculty of Science, The University of Tokyo, Bunkyo‐ku, Tokyo, Japan
- ↵*
Corresponding author. Tel: +81 55 981 6807; E‐mail: soinagak{at}nig.ac.jp
Corresponding author. Tel: +81 55 981 6801; Fax: +81 55 981 6804; E‐mail: tkakutan{at}nig.ac.jp
A genetic interaction between histone demethylases IBM1 and LDL2 reveals that H3K9 methylation in gene bodies induces transcriptional silencing by triggering the loss of H3K4 monomethylation.
Synopsis
A genetic interaction between histone demethylases IBM1 and LDL2 reveals that H3K9 methylation in gene bodies induces transcriptional silencing by triggering the loss of H3K4 monomethylation.
A mutation in putative H3K4 demethylase LDL2 suppresses the developmental defects seen in the Arabidopsis mutant of H3K9 demethylase IBM1.
LDL2 functions downstream of ibm1‐induced ectopic H3K9 dimethylation in gene bodies to decrease H3K4me1 levels and repress gene expression.
The gene‐body localized H3K9me2 mark represses expression of TEs via demethylation of H3K4me1.
Counteracting demethylation of H3K9me2 and H3K4me1, together with transcription, can induce differentiation of active and inactive transcription units.
The EMBO Journal (2017) 36: 970–980
- Received June 9, 2016.
- Revision received December 14, 2016.
- Accepted December 16, 2016.
- © 2017 The Authors
- DNA sequence properties that predict susceptibility to epiallelic switching
- Marco Catoni1,2,
- Jayne Griffiths1,
- Claude Becker3,
- Nicolae Radu Zabet1,5,
- Carlos Bayon1,
- Mélanie Dapp2,
- Michal Lieberman‐Lazarovich2,4,
- Detlef Weigel3 and
- Jerzy Paszkowski (jerzy.paszkowski{at}slcu.cam.ac.uk)*,1,2
- 1The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- 2Department of Plant Biology, University of Geneva, Geneva, Switzerland
- 3Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- 4The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University, Rohovot, Israel
- 5School of Biological Sciences, University of Essex, Colchester, UK
- ↵*Corresponding author. Tel: +44 1223 761159; E‐mail: jerzy.paszkowski{at}slcu.cam.ac.uk
Why certain loci are able to stably switch between alternative epigenetic states (forming heritable epialleles), while others remain resistant to such switches seems to be predetermined by their genetic features, such as DNA sequence composition and repetitiveness.
Synopsis
Why certain loci are able to stably switch between alternative epigenetic states (forming heritable epialleles), while others remain resistant to such switches seems to be predetermined by their genetic features, such as DNA sequence composition and repetitiveness.
Low‐copy number loci enriched in CG dinucleotides form transgenerationally stable epialleles.
High‐copy number loci depleted of CG nucleotides rapidly revert to one epiallelic form.
The EMBO Journal (2017) 36: 617–628
- Received September 9, 2016.
- Revision received December 9, 2016.
- Accepted December 9, 2016.
- © 2017 The Authors. Published under the terms of the CC BY NC ND 4.0 license
This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs 4.0 License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
- TFIID or not TFIID, a continuing transcriptional SAGA
Eukaryotic protein‐coding genes are typically classified into two groups: those with expression regulated by specific signals versus the relatively constant “housekeeping” genes. Although these differences are associated with alternative modes of RNA polymerase II (RNAP II) pre‐initiation complex (PIC) assembly, a role for gene‐specific activators in controlling “regulatability” has been difficult to rule out. To address this question, de Jonge et al (2017) studied a group of genes controlled by a common activator but dependent on either TFIID or SAGA and found that the magnitude of regulation strongly correlates with the mechanism of PIC assembly.
See also: WJ de Jonge et al (February 2017)
Alternative modes of transcriptional pre‐initiation complex assembly rather than gene‐specific activators differentiate housekeeping gene expression from regulated gene expression.
- © 2017 The Authors
- Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter
- Rodrigo Arias‐Cartin1,2,
- Genevieve S Dobihal1,3,5,
- Manuel Campos1,2,3,
- Ivan V Surovtsev1,2,3,
- Bradley Parry1,2 and
- Christine Jacobs‐Wagner (christine.jacobs-wagner{at}yale.edu)*,1,2,3,4
- 1Microbial Sciences Institute, Yale University, West Haven, CT, USA
- 2Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
- 3Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
- 4Department of Microbial Pathogenesis, Yale Medical School, Yale University, New Haven, CT, USA
- 5Present Address: Department of Microbiology and Immunology, Harvard Medical School, Boston, MA, USA
- ↵*Corresponding author. Tel: +1 203 737 7219; E‐mail: christine.jacobs-wagner{at}yale.edu
Experiments and modeling reveal a simple mechanism by which DNA replication can control spatiotemporal dynamics of bacterial DNA‐binding proteins involved in chromosome organization and global gene expression.
Synopsis
Nucleoid‐associated proteins (NAPs) regulate chromosome organization and global gene expression in bacteria. Experiments and modeling reveal a simple mechanism by which DNA replication can control the spatiotemporal dynamics of NAPs and other DNA‐binding proteins.
GapR is an α‐proteobacterial NAP that affects growth, division, DNA replication, and global gene expression in Caulobacter crescentus.
DNA‐binding and transcriptional activities of GapR are biased from origin to terminus regions of the chromosome despite uniformly distributed binding sites.
GapR binds strongly to DNA in vivo, and dissociation is primarily driven by replication fork progression.
Modeling shows that the directionality of DNA replication causes the origin‐to‐terminus asymmetry in DNA‐binding activity.
The EMBO Journal (2017) 36: 301–318
- Received August 16, 2016.
- Revision received November 29, 2016.
- Accepted November 30, 2016.
- © 2016 The Authors
- Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
- Wim J de Jonge1,2,†,
- Eoghan O'Duibhir1,3,†,
- Philip Lijnzaad1,2,
- Dik van Leenen1,
- Marian JA Groot Koerkamp1,2,
- Patrick Kemmeren1,2 and
- Frank CP Holstege (f.c.p.holstege{at}prinsesmaximacentrum.nl)*,1,2
- 1Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- 2Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- 3Present Address: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
- ↵*Corresponding author. Tel: +31 88 972 72 72; E‐mail: f.c.p.holstege{at}prinsesmaximacentrum.nl
↵† These authors contributed equally to this work
The different level of responsiveness seen for housekeeping vs. regulatable gene promoters is inherent to the underlying DNA sequence rather than to specific activator use.
Synopsis
Responsiveness, a property that distinguishes housekeeping from regulatable genes, is inherent to core promoter class rather than to activator use. The molecular mechanisms underlying regulatability include various types of negative regulation.
Molecular mechanisms at DNA sequence level distinguish housekeeping genes from regulatable genes.
Responsiveness is inherent to the core promoter type.
SAGA‐dominated/TATA‐like promoters are more responsive to activator presence.
Increased activator response is due to TBP removal by Mot1 and nucleosome repositioning.
The EMBO Journal (2017) 36: 274–290
- Received August 31, 2016.
- Revision received October 18, 2016.
- Accepted November 1, 2016.
- © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license
This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs 4.0 License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
- Cohesin acetylation and Wapl‐Pds5 oppositely regulate translocation of cohesin along DNA
- Mai Kanke1,
- Eri Tahara1,
- Pim J Huis in't Veld2,3 and
- Tomoko Nishiyama (nishiyama{at}bio.nagoya-u.ac.jp)*,1
- 1Division of Biological Science, Graduate School of Science Nagoya University, Nagoya, Japan
- 2Research Institute of Molecular Pathology, Vienna, Austria
- 3Max Planck Institute for Molecular Physiology, Dortmund, Germany
- ↵*Corresponding author. Tel: +81 52 747 6591; E‐mail: nishiyama{at}bio.nagoya-u.ac.jp
Single‐molecule observations of cohesin translocation in vitro and in Xenopus egg extracts define its dependence on regulatory factors and DNA replication.
Synopsis
Single‐molecule observations of individual cohesin rings on DNA define how regulatory factors such as acetylation, Wapl‐Pds5, and Sororin, as well as DNA replication influence cohesin translocation in vitro and in Xenopus egg extracts.
Scc2‐Scc4‐dependent topological loading of cohesin is required for cohesin translocation along DNA.
Acetylation of cohesin by Esco1 (or Xenopus XEco2) promotes cohesin translocation along DNA and chromatin.
Cohesin translocation is suppressed by Wapl‐Pds5 and Sororin, and facilitated by Aurora B‐mediated phosphorylation.
Cohesin is preferentially present and translocated in nucleosome‐poor region of unreplicated chromatin.
Upon DNA replication, cohesin is either (i) stalled and incorporated into replicating DNA, (ii) translocated with replication, or (iii) dissociated from replicating DNA.
The EMBO Journal (2016) 35: 2686–2698
- Received September 19, 2016.
- Revision received November 4, 2016.
- Accepted November 7, 2016.
- © 2016 The Authors
- Rapid movement and transcriptional re‐localization of human cohesin on DNA
- Iain F Davidson1,
- Daniela Goetz1,†,
- Maciej P Zaczek1,†,
- Maxim I Molodtsov1,2,†,
- Pim J Huis in 't Veld1,5,
- Florian Weissmann1,
- Gabriele Litos1,
- David A Cisneros1,6,
- Maria Ocampo‐Hafalla3,
- Rene Ladurner1,7,
- Frank Uhlmann3,
- Alipasha Vaziri1,2,4,‡ and
- Jan‐Michael Peters (peters{at}imp.ac.at)*,1
- 1Research Institute of Molecular Pathology (IMP), Vienna, Austria
- 2Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- 3The Francis Crick Institute, London, UK
- 4The Rockefeller University, New York, NY, USA
- 5Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- 6 The Laboratory for Molecular Infection Medicine Sweden (MIMS) and Department of Molecular Biology, Umeå University, Umeå, Sweden
- 7 Department of Biochemistry, Stanford University, Stanford, CA, USA
- ↵*Corresponding author. Tel: +43 1797303000; E‐mail: peters{at}imp.ac.at
↵† These authors contributed equally to this work
Human cohesin rings entrap DNA and rapidly translocate along DNA by diffusion. Cohesin can pass over small DNA‐bound proteins but is constrained in its movement by transcription and DNA‐bound CCCTC‐binding factor (CTCF).
Synopsis
Human cohesin rings entrap DNA and rapidly translocate along DNA by diffusion. Cohesin can pass over small DNA‐bound proteins but is constrained in its movement by transcription and DNA‐bound CCCTC‐binding factor (CTCF).
Single‐molecule imaging of cohesin bound to immobilized DNA reveals that cohesin binds to DNA in a salt‐resistant manner and translocates with a diffusion coefficient higher than many other DNA‐binding proteins (1.72 ± 0.1 µm2/s).
Cohesin is released from DNA following cleavage of DNA or the cohesin ring, consistent with topological entrapment.
Cohesin can diffuse past obstacles with a diameter < ˜11 nm, including nucleosomes, but not those with a diameter > ˜21 nm, such as QDots.
CTCF constrains the movement of cohesin.
Transcribing T7 RNA polymerase provides directionality to cohesin.
The EMBO Journal (2016) 35: 2671–2685
- Received August 3, 2016.
- Revision received September 8, 2016.
- Accepted October 3, 2016.
- © 2016 The Authors. Published under the terms of the CC BY 4.0 license
This is an open access article under the terms of the Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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