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`Volume 33 Number 22 | 18 November 2014
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`

`

`The EMBOJ'Oflrfla'J' VOL 33 | NO 22 | 2014
`emboiembopressorg
`
`Table ofcontents
`
`Ednoflal
`
`2597
`
`Transparent, Reproducible Data
`Bernd Pulverer
`
`Haveyouseen?
`
`Tllli
`
`JOURNAL
`
`EMBO
`
`6° a.a0
`
`2598
`
`Shigell‘u hacks host immune responses by reprogramming the host
`epigenome
`Hiroshi Ashida &Chihiro Sasakawa
`
`2601
`
`Splicing together sister chromatids
`Juan Valcarcel & Marcos Malumbres
`
`Have you seen? 2598
`
`2604 Old dog, new tricks: Arfl required for mitochondria homeostasis
`Catherine Rabouille
`
`Articles
`
`2606
`"'j‘
`
`Shigel'l'o flexneri targets the HP17subcode through the
`phosphothreonine lyase OspF
`Habiba Harouz. Christophe Rachez. Benoit M Meijer, BenOit Marteyn.
`Francome Donnadieu, Florence Commas. Christian Muchardt,
`Philippe Sansonetti & Laurence Arbibe
`
`2623
`Q,
`.74
`
`Functional genomic: identifies a requirement of pre-mRNA splicing
`factors for sisterchromatid cohesion
`Sriramkumar Sundaramoorthy, Maria Dolores Vézquez-Novelle,
`Sergey Lekomtsev, Michael Howell & Mark Petronczki
`
`2643
`”j"
`
`"
`
`SNWI enables sister chromatid cohesion by mediating the splicing of
`sororin and APCZ pre-mRNAs
`Petra van der Lelii, Roman R Stocsits. Rene Ladurner. Georg Petzold.
`Emanuel Kreidl. Birgit Koch. Julia Schmitz, Beate Neumann, Jan Ellenberg
`&ian-Mrchael Peters
`
`2659 The small GTPase Arfl modulates mitochondrial morphology
`. K.“
`and function
`
`Karin B Ackema,JUrgen Hench. Stefan Bbckler. Shyi Chyi Wang.
`Ursula Sauder, Heidi Mergentaler, Benedikt Westermann‘ Frederic Bard,
`Stephan Frank 31 Anne Spa ng
`
`Chromatin, Epigenetics. Genomics ii.
`Functional benomics; Microbiology.
`
`Virology & Host Pathogen interaction
`
`DNA Replication. Repair 8t Recombn'ianon:
`RNA BiologyI
`
`DNA Replication, Repair 8.. Recombination:
`RNA Biology
`
`Membrane EL Intracellular Transport
`
`2676
`3.3
`
`n
`
`OPA1~dependent cristae modulation is essential for cellular adaptation
`to metabolic demand
`
`Membrane & Intracellular Transport:
`Metabolism
`
`David A Patten. Jacob Wong, Mireille Khacho. Vincent Soubannier.
`Ryan ] Mailloux. Karine PilonvLarose, Jason C MacLaurin. David S Park.
`Heidi M McBride, Laura Trinkle'Mulcahy. Mary—Ellen Harper.
`Marc Germain EL Ruth 5 Slack
`
`

`

`The EMBO)ourriai VOL 33 | NO 2 212014
`embojembopressorg
`
`2692 Crystal structure ofa c-di-AMP riboswitch reveals an internally
`”13‘
`pseudo-dimeric RNA
`Christopher P Jones &Adrian R Ferré-D’Amaré
`
`RNA Biology; Structural Biology
`
`2704
`Etc. ”.1?
`
`'“hibit0r'3 ensures biPolar mitotic spindle attachment by limiting
`association of 50522 with kinetochore—bound protein phosphatase-1
`Annika Eiteneuer. Jonas Seiler. Matthias Weith. Monique Beullens. Bart Lesage.
`Veronica Krenn.i\ndrea Musacchio. Mathieu Boiler: iii-lemma Meyer
`
`Cell Cycle; Post- translational Modifications.
`.
`.
`Proteolysis 8t Proteornics
`
`2721
`”i.”
`
`Peripheral natural killercell maturation depends on the transcription
`factor Aiolos
`
`lranIUflfllOt’J: TianSUIPilfln
`
`Melissa L Holmes. Nicholas D Huntington Rebecca PLThong. Jason Brady.
`Yoshihiro HElyakawa. Christopher E Andoniou. Peter Fleming. Wei Shi. Gordon
`K Sniyth. Mariapia A Degli-Espogti. Gabrielle T Belz. Axel Kallies. Sebastian
`Carotta, Mark] Smyth & Stephen L Nutt
`
`Corrigendurn
`
`2735
`
`Tubulin glycylases are required for primary cilia, control ofcell
`proliferation and tumordevelopment in colon
`Cecilia Rocha. Laura Papon. Wulfran Cache-uni. Patricia Marques Sousa,Valeria
`Lascano. Olivia Tort. Tiziana Giordano. Sophie Vacher, Benedicte Lemmers.
`Pascale Mariani, Didier Meseure,ian Paul Medema. Ivan Bieche. Michael
`Hahne &Carstenjanke
`
`I”- Open-accesstirlltledislrihutt-tl under Illl'lf_'llll'.ril ,ir Min-a.- r lIIT‘IIIl‘III'JI\Il[|r1l”.l'i|l i ir enac-
`Source Dala; figures are mntpletnented by pi ”nary tiara
`V,’ Transparent Process: tintinvrnciusi'isleree Ft'ptilT'wlnd utliinmili'r'iurlmi r urir_--,priiirlr:itr r: -1l"
`published alongstde the research article
`
`Cover: The Mechanicsol Bacteriophage I-l —ll1eanist,ianice with}; r; ,3 medicalinr n-nlilir
`illustrator and animator (steampunl: _mecl icalthh: II.I‘ll:‘ll Imm} lit-r [)(l'.‘sllill‘. Il'li. ludr: r: iinliining
`cr'eatwrty, lll'lagll'lflllt‘lll,afld scienceto create engaging Imageslanlce writes about I'I'II'. irndflt.
`"Initially when i started composing this piece in 3D. I wanted a more 'natural' environment
`that is more typical ofmedical all. However. i was socaptivated bvthe'mechanical' nature of
`the bacteriophage T4 that I jUS'L' ran with the idea and created something more original with
`a Steampu nk look and Feel. i wanted it to look as ifsomeunc- sat at higherdesk and worked
`meticulously in constructing an actual bacteriophage. fashioned from hits and pieces of scraps
`salvaged from all different sources. Despitethesteampunk look,l took care ll'i ensuringthat the
`bacteriophage is accurately represented, eg.its head is icosahedral with all the surface [)ftltlflll'.
`{gp24. Hoc. etc) represented. albeit. in scrap metal."
`
`

`

`This material may be protected by Copyright law (Title 17 U.S. Code)
`
`Editorial
`
`THE
`
`JOURNAL
`
`EMBO
`
`Transparent, Reproducible Data
`
`Bernd Pulverer
`
`reporting of
`the
`for
`New guidelines
`research and source data enhance the
`
`and
`interpretation
`published research.
`
`reproducibility
`
`of
`
`Source Data—a new dimension for
`
`research papers
`
`lte scientific researclt paper retnains
`tlte main mode of sharing scientific
`aspects
`information.
`Two
`key
`contribute to [lie unabated success of this
`
`l'ornlat. despite the myriad possibilities ior
`new ways In share research in an oltliite
`world:
`validation
`by
`independent
`peer
`review and the instaposition ol'
`researclt
`results
`presented in figures.
`tables. and
`Videos witlt
`Ihe .utlhors'
`Iestllal
`interpre-
`tation of
`these results. For many years.
`publishers have focused largely on rendering
`test
`for pttblicatiott attd search ettgittes are
`limited to indesing the title. abstract. intro-
`duction,
`results, methods and discussion
`sections of a paper. Yet. the claims made in
`.I paper rely on data selected by the authors
`attd synthesized into tigures lltal
`illustrate
`tlte fimiings for the human reader. Figures
`are tlte heart of tile paper altd sltnultl npetl a
`Vista on tlte research data. Uldorlttualely.
`that view is currently often limited to data
`\‘istialimtious
`.tttd
`illuslrations. As we
`
`hare reported previously tl.etttbet'gt‘t’. llllfl'.
`JtIt-IaJu. we
`l'tilcerer.
`encourage
`file
`presentation til Sillll'l'e llata.
`.‘llltl
`ittdeed
`links to Source llala are already available in
`many figures itt
`the inurttal. Source llala
`ltl'tlt'itlt's‘
`access
`to minimally processed
`\‘t'l'slttlls ot
`the data umlerlying figures such
`as data tiles used to plot graphs and experi-
`mental replicates or less cropped versions of
`reptesetitative data shown iii a figure panel.
`Source llata can also include higher resolu-
`tion
`data
`IeIIdeI'ings
`of
`compressed itt
`Iigutes lot etticiem downloading.
`
`Source llata pt'm-‘ides a inundation to a
`paper tltat at'i'ortls a much richer \‘lt‘\\' of the
`tindings discussed aml enables reanalysis
`and reuse lit'
`the interested reader. as well
`[The data
`
`are
`access.
`as computational
`.tlsn
`it
`license]
`[‘C-tl
`a
`pttblislted uttder
`provides all efficient means to archive data
`itt close iustaposition with the paper that
`discusses the findings.
`A central tettet of publishing is to ensure
`I'eprntltlcibililt'. This requires the transparent
`amt detailed reporting aml sharing not only
`of the data. but also the underlying methods
`and reagents. Our goal is to develop method
`sections that satisfy these conditions. includ-
`ing detailed experimental protocols
`and
`reagents that can be identified unambigu-
`ously. attd which link directly to the relevant
`figure panels and data, We are conscious
`that these enhancements will need to tie into
`the
`
`det'elnpltient
`tools
`management
`of
`this
`information
`
`of
`laboratory
`digital
`tltal
`allow submission
`without
`unreasonabh'
`
`burtlening the autltors.
`
`checklist for reporting life sciences
`research
`
`This
`
`iottrltal
`
`attd its
`
`three
`
`I-Ia-tntl
`
`Press
`
`for
`siblings have introduced a Checklist
`Authors itt order to enhance attd standardize
`
`the reporting of key information it: research
`papers aitd to support reanalysis attd repeti-
`tiott
`of experiments
`try
`the community.
`Reporting standards are well established in
`clinical research; the aim of this checklist
`is
`
`to consistently capture essential information
`itt preclinical
`research atid to ensure that
`authors. editors. aitd referees can cross
`check
`eilicielltlt' whether
`these
`basic
`
`requirements for reporting reliable research
`have been met. While completion of the list
`at
`initial submission is welcome. we only
`
`require coittpletiott upon revision of a manu
`script
`.t stage when publication is highly
`
`likelr
`
`at
`
`The
`
`l-ft‘rltitl
`
`.tntn'nul
`
`tl’nh'erer.
`
`require-
`the checklist highlights
`Ant-Ia}.
`ments from the iotll'ltal‘s guide to authors
`that are often overlooked.
`including key
`information for figure panels .nnl captions.
`appropriate statistical treatment for data, tlte
`reporting of
`reagents, animal models and
`
`lttiman subiectderived data. as well as guid-
`attce to optimize data accessibility. The
`locus is on the molecular and cell biological
`research I\_'pica|l\'
`reported lit The tut-'ilir}
`.tottrnnt'.
`
`to guidance
`similar
`is
`checklist
`‘l'he
`issued by a tnttnber other ionrnals. ittcludittg
`Nature and Science.
`it is consistent with the
`Guidelines
`for
`
`Reporting
`attd
`Principles
`published this month
`l'reclinical Research
`bt' a group of iournals including the four
`iiMliO l’ress iourttals. The principles were
`agreed at
`a workshop held under
`the
`auspices of
`the NIH earlier this summer.
`where it was agreed that
`tuttrnals have a
`responsibility to act as gatekeepers for a reii
`able literature.
`
`Please review the checklist even if you
`
`for publica-
`are not preparing a manuscript
`tion at this time
`the pnittts highlighted will
`help inform the planning of a successful
`research
`protect wherever you
`plan
`to
`submit your results. Please also regard this
`as a
`living document we hope to obtain
`rout feedback to add to attd revise the tutor
`
`intended to
`is
`mation perimticalh'. The list
`help our authots publish transparent and
`reproducible research papers; it
`is emphati
`calit‘ not
`to make the publication process
`more cumbersome.
`
`References
`Lentbergcr l (2010} Hunt bench to wett'ate Moi
`Syn Biol 6: ate
`PtIlVCI‘Ct
`Ii [2014M EMBU Pr'CS'S
`publish. {MSG} 33: l
`2
`Pulvcrcr [l Pill/lb} SIN" t‘litntl'. [rt-130] if}
`128';
`1286
`
`a new way to
`
`IMItrJ. tit-trtt-ItJt-tg, | .r‘tnmtty I marl
`UOI I’Jl't."i_’."etttb|.’fll-i‘1'.l.‘.-‘>i
`
`[ternd PttIverett’u‘ert‘botnutnotorg
`
`.'tl] i the Atultiu
`
`this material wascopled
`at the NLM and may be
`Subject US Copyright Laws
`
`liti- r'a’t-ltit‘) tumour Vol is | No 2.2 I )ti'l-i
`
`2597
`
`