Selected Edited Manuscripts

2017

Dynamic subunit turnover in ESCRT-III assemblies is regulated by Vps4 to mediate membrane remodelling during cytokinesis.

Mierzwa BE, Chiaruttini N, Redondo-Morata L, Moser von Filseck J, König J, Larios J, Poser I, Müller-Reichert T, Scheuring S, Roux A, Gerlich DW.
Nat Cell Biol. 2017

Plants transfer lipids to sustain colonization by mutualistic mycorrhizal and parasitic fungi.

Jiang Y, Wang W, Xie Q, Liu N, Liu L, Wang D, Zhang X, Yang C, Chen X, Tang D, Wang E.
Science. 2017 Jun 8

RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding.

Knuckles P, Carl SH, Musheev M, Niehrs C, Wenger A, Bühler M.
Nat Struct Mol Biol. 2017 Jun 5.

MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality.

Weiser NE, Yang DX, Feng S, Kalinava N, Brown KC, Khanikar J, Freeberg MA, Snyder MJ, Csankovszki G, Chan RC, Gu SG, Montgomery TA, Jacobsen SE, Kim JK.
Dev Cell. 2017 May 22;41(4):408-423

Interaction between Tumor Cell Surface Receptor RAGE and Proteinase 3 Mediates Prostate Cancer Metastasis to Bone.

Kolonin MG, Sergeeva A, Staquicini DI, Smith TL, Tarleton CA, Molldrem JJ, Sidman RL, Marchiò S, Pasqualini R, Arap W.
Cancer Res. 2017 Apr 20

M1-like monocytes are a major immunological determinant of severity in previously healthy adults with life-threatening influenza.

Cole SL, Dunning J, Kok WL, Benam KH, Benlahrech A, Repapi E, Martinez FO, Drumright L, Powell TJ, Bennett M, Elderfield R, Thomas C, Dong T, McCauley J, Liew FY, Taylor S, Zambon M, Barclay W, Cerundolo V, Openshaw PJ, McMichael AJ, Ho LP.
JCI Insight. 2017 Apr 6;2(7). pii: 91868

Efficient Generation of diRNAs Requires Components in the Posttranscriptional Gene Silencing Pathway.

Miki D, Zhu P, Zhang W, Mao Y, Feng Z, Huang H, Zhang H, Li Y, Liu R, Zhang H, Qi Y, Zhu JK.
Sci Rep. 2017 Mar 22;7(1):301

A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice.

Zhang L, Yu H, Ma B, Liu G, Wang J, Wang J, Gao R, Li J, Liu J, Xu J, Zhang Y, Li Q, Huang X, Xu J, Li J, Qian Q, Han B, He Z, Li J.
Nat Commun. 2017 Mar 20;8:14789.

Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance.

Deng Y, Zhai K, Xie Z, Yang D, Zhu X, Liu J, Wang X, Qin P, Yang Y, Zhang G, Li Q, Zhang J, Wu S, Milazzo J, Mao B, Wang E, Xie H, Tharreau D, He Z.
Science. 2017 Mar 3;355(6328):962-965.

Human Papillomavirus 16 E6 Up-regulates APOBEC3B via the TEAD Transcription Factor

Mori S, Takeuchi T, Ishii Y, Yugawa T, Kiyono T, Nishina H and Kukimoto, I
J. Virol. March 2017 91:e02413-16

m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition.

Zhao BS, Wang X, Beadell AV, Lu Z, Shi H, Kuuspalu A, Ho RK, He C.
Nature. 2017 Feb 23;542(7642):475-478


2016

A Surveillance Mechanism Ensures Repair of DNA Lesions during Zygotic Reprogramming

Ladstätter S, Tachibana-Konwalski K.
Cell 2016 Dec 15;167(7):1774-1787.

A pair of transposon-derived proteins function in a histone acetyltransferase complex for active DNA demethylation.

Duan CG, Wang X, Xie S, Pan L, Miki D, Tang K, Hsu CC, Lei M, Zhong Y, Hou YJ, Wang Z, Zhang Z, Mangrauthia SK, Xu H, Zhang H, Dilkes B, Tao WA, Zhu JK.
Cell Res. 2016 Dec 9.

MicroRNA-34/449 controls mitotic spindle orientation during mammalian cortex development.

Fededa JP, Esk C, Mierzwa B, Stanyte R, Yuan S, Zheng H, Ebnet K, Yan W, Knoblich JA, Gerlich DW.
EMBO J. 2016 Nov 15;35(22):2386-2398.

The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications.

Tang K, Lang Z, Zhang H, Zhu JK.
Nat Plants. 2016 Oct 31;2(11):16169.

Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole.

Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A, Kraft C.
Molecular Cell. 2016 Oct 20;64(2):221-235.

High-throughput allele-specific expression across 250 environmental conditions

MoyerbraileanG, Richards A, Kurtz D, Kalita C, Davis G, Harvey C, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, Luca F.
Genome Res. 2016. Oct. 19 epub ahead of print.

Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition.

Bazzini AA, Del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ.
EMBO J. 2016 Oct 4;35(19):2087-2103.

Linear ubiquitination by LUBEL has a role in Drosophila heat stress response

Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F.
EMBO Reports. 2016 Oct 4; 

Sphingomyelin-induced inhibition of the plasma membrane calcium ATPase causes neurodegeneration in type A Niemann-Pick disease.

Pérez-Cañamás A, Benvegnù S, Rueda CB, Rábano A, Satrústegui J, Ledesma MD.
Mol Psychiatry. 2016 Sep 13.

Aging Triggers a Repressive Chromatin State at Bdnf Promoters in Hippocampal Neurons.

Palomer E, Martín-Segura A, Baliyan S, Ahmed T, Balschun D, Venero C, Martin MG, Dotti CG.
Cell Rep. 2016 Sep 13;16(11):2889-900.

c-Fos Repression by Piwi Regulates Drosophila Ovarian Germline Formation and Tissue Morphogenesis.

Klein JD, Qu C, Yang X, Fan Y, Tang C, Peng JC.
PLoS Genet. 2016 Sep 13;12(9):e1006281.

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity.

Mair B, Konopka T, Kerzendorfer C, Sleiman K, Salic S, Serra V, Muellner MK, Theodorou V, Nijman SM.
PLoS Genet. 2016 Sep 2;12(9):e1006279.

The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism.

Zhang Q, Li Y, Xu T, Srivastava AK, Wang D, Zeng L, Yang L, He L, Zhang H, Zheng Z, Yang DL, Zhao C, Dong J, Gong Z, Liu R, Zhu JK.
Cell Discov. 2016 Aug 9;2:16027

Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation.

Zhang Q, Wang D, Lang Z, He L, Yang L, Zeng L, Li Y, Zhao C, Huang H, Zhang H, Zhang H, Zhu JK.
Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4248-56.

Ki-67 acts as a biological surfactant to disperse mitotic chromosomes.

Cuylen S, Blaukopf C, Politi AZ, Müller-Reichert T, Neumann B, Poser I, Ellenberg J, Hyman AA, Gerlich DW.
Nature. 2016 Jun 29.

Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells.

Itahana Y, Zhang J, Göke J, Vardy LA, Han R, Iwamoto K, Cukuroglu E, Robson P, Pouladi MA, Colman A, Itahana K.
Sci Rep. 2016 Jun 27;6:28112.

Mechanotransduction activates canonical Wnt/β-catenin signaling to promote lymphatic vascular patterning and the development of lymphatic and lymphovenous valves.

Cha B, Geng X, Mahamud MR, Fu J, Mukherjee A, Kim Y, Jho EH, Kim TH, Kahn ML, Xia L, Dixon JB, Chen H, Srinivasan RS.
Genes Dev. 2016 Jun 15;30(12):1454-69.

Brain endothelial cell-targeted gene therapy of neurovascular disorders.

Marchiò S, Sidman RL, Arap W, Pasqualini R.
EMBO Mol Med. 2016 Jun 1;8(6):592-4.

RANKL/RANK control Brca1 mutation-driven mammary tumors.

Sigl V, Owusu-Boaitey K, Joshi PA, Kavirayani A, Wirnsberger G, Novatchkova M, Kozieradzki I, Schramek D, Edokobi N, Hersl J, Sampson A, Odai-Afotey A, Lazaro C, Gonzalez-Suarez E, Pujana MA, Cimba F, Heyn H, Vidal E, Cruickshank J, Berman H, Sarao R, Ticevic M, Uribesalgo I, Tortola L, Rao S, Tan Y, Pfeiler G, Lee EY, Bago-Horvath Z, Kenner L, Popper H, Singer C, Khokha R, Jones LP, Penninger JM.
Cell Res. 2016 Jul;26(7):761-74.

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila.

Upadhyay M, Martino Cortez Y, Wong-Deyrup S, Tavares L, Schowalter S, Flora P, Hill C, Nasrallah MA, Chittur S, Rangan P.
PLoS Genet. 2016 Mar 28;12(3):e1005918.

Transglutaminase 2 contributes to a TP53-induced autophagy program to prevent oncogenic transformation.

Yeo SY, Itahana Y, Guo AK, Han R, Iwamoto K, Nguyen HT, Bao Y, Kleiber K, Wu YJ, Bay BH, Voorhoeve M, Itahana K
Elife. 2016 Mar 9;5. pii: e07101.

Specific Inhibition of β-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein.

Ben Halima S, Mishra S, Raja KM, Willem M, Baici A, Simons K, Brüstle O, Koch P, Haass C, Caflisch A, Rajendran L.
Cell Rep. 2016 Mar 8;14(9):2127-41.

AAVP displaying octreotide for ligand-directed therapeutic transgene delivery in neuroendocrine tumors of the pancreas.

Smith TL, Yuan Z, Cardó-Vila M, Sanchez Claros C, Adem A, Cui MH, Branch CA, Gelovani JG, Libutti SK, Sidman RL, Pasqualini R, Arap W.
Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):2466-71

Self-targeting of TNF-releasing cancer cells in preclinical models of primary and metastatic tumors.

Dondossola E, Dobroff AS, Marchiò S, Cardó-Vila M, Hosoya H, Libutti SK, Corti A, Sidman RL, Arap W, Pasqualini R.
Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2223-8

Dicer-independent RNA-directed DNA methylation in Arabidopsis.

Yang DL, Zhang G, Tang K, Li J, Yang L, Huang H, Zhang H, Zhu JK.
Cell Res. 2016 Jan;26(1):66-82.

Sex-specific silencing of X-linked genes by Xist RNA

Gayen S, Maclary E, Hinten M, Kalantry S.
Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):E309-18.

MBC

Actin- and microtubule-dependent regulation of Golgi morphology by FHDC1.

Copeland SJ, Thurston SF, Copeland JW
Mol Biol Cell. 2016 Jan 15;27(2):260-76

Multiple mouse models of primary lymphedema exhibit distinct defects in lymphovenous valve development.

Geng X, Cha B, Mahamud MR, Lim KC, Silasi-Mansat R, Uddin MK, Miura N, Xia L, Simon AM, Engel JD, Chen H, Lupu F, Srinivasan RS
Dev Biol. 2016 Jan 1;409(1):218-33


2015

Light-assisted small-molecule screening against protein kinases.

Inglés-Prieto Á, Reichhart E, Muellner MK, Nowak M, Nijman SM, Grusch M, Janovjak H.
Nat Chem Biol. 2015 Dec;11(12):952-4.

CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo.
Nat Methods. 2015 Oct;12(10):982-8.

Transformation of enriched mammary cell populations with polyomavirus middle T antigen influences tumor subtype and metastatic potential.

Drobysheva D, Smith BA, McDowell M, Guillen KP, Ekiz HA, Welm BE.
Breast Cancer Res. 2015 Oct 1;17(1):132.

Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise.

Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi L, Sivak D, Thomson M.
Cell Systems. 2015 Aug 26;1(2):117-129.

TRIM28 Is an E3 Ligase for ARF-Mediated NPM1/B23 SUMOylation That Represses Centrosome Amplification.

Neo SH, Itahana Y, Alagu J, Kitagawa M, Guo Ak, Lee SH, Tang K, Itahana K.
MCB. 2015, Aug;35(16):2851-63.

Targeting the interleukin-11 receptor α in metastatic prostate cancer: A first-in-man study.

Pasqualini R, Millikan RE, Christianson DR, Cardó-Vila M, Driessen WH, Giordano RJ, Hajitou A, Hoang AG, Wen S, Barnhart KF, Baze WB, Marcott VD, Hawke DH, Do KA, Navone NM, Efstathiou E, Troncoso P, Lobb RR, Logothetis CJ, Arap W.
Cancer. 2015 Jul 15;121(14):2411-21.

PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3.

Salameh A, Lee AK, Cardó-Vila M, Nunes DN, Efstathiou E, Staquicini FI, Dobroff AS, Marchiò S, Navone NM, Hosoya H, Lauer RC, Wen S, Salmeron CC, Hoang A, Newsham I, Lima LA, Carraro DM, Oliviero S, Kolonin MG, Sidman RL, Do KA, Troncoso P, Logothetis CJ, Brentani RR, Calin GA, Cavenee WK, Dias-Neto E, Pasqualini R, Arap W.
Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8403-8.

A primary role for the Tsix lncRNA in maintaining random X-chromosome inactivation.

Gayen S, Maclary E, Buttigieg E, Hinten M, Kalantry S
Cell Rep. 2015 May 26;11(8):1251-65.

The BASL polarity protein controls a MAPK signaling feedback loop in asymmetric cell division.

Zhang Y, Wang P, Shao W, Zhu JK, Dong J.
Dev Cell. 2015 Apr 20;33(2):136-49.

The Paf1 complex represses small-RNA-mediated epigenetic gene silencing.

Kowalik KM, Shimada Y, Flury V, Stadler MB, Batki J, Bühler M.
Nature. 2015 Apr 9;520(7546):248-52.

An anti-ubiquitin antibody response in transitional cell carcinoma of the urinary bladder.

Ardelt PU, Ebbing J, Adams F, Reiss C, Arap W, Pasqualini R, Bachmann A, Wetterauer U, Riedmiller H, Kneitz B.
PLoS One. 2015 Mar 5;10(3):e0118646.

Ligand-directed targeting of lymphatic vessels uncovers mechanistic insights in melanoma metastasis.

Christianson DR, Dobroff AS, Proneth B, Zurita AJ, Salameh A, Dondossola E, Makino J, Bologa CG, Smith TL, Yao VJ, Calderone TL, O’Connell DJ, Oprea TI, Kataoka K, Cahill DJ, Gershenwald JE, Sidman RL, Arap W, Pasqualini R.
Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2521-6.

The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing.

Lang Z, Lei M, Wang X, Tang K, Miki D, Zhang H, Mangrauthia SK, Liu W, Nie W, Ma G, Yan J, Duan CG, Hsu CC, Wang C, Tao WA, Gong Z, Zhu JK.
Mol Cell. 2015 Mar 19;57(6):971-83.

Targeting a cell state common to triple-negative breast cancers.

Muellner MK, Mair B, Ibrahim Y, Kerzendorfer C, Lechtermann H, Trefzer C, Klepsch F, Müller AC, Leitner E, Macho-Maschler S, Superti-Furga G, Bennett KL, Baselga J, Rix U, Kubicek S, Colinge J, Serra V, Nijman SM.
Mol Syst Biol. 2015 Feb 19;11(1):789.

An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis.

Li Y, Córdoba-Cañero D, Qian W, Zhu X, Tang K, Zhang H, Ariza RR, Roldán-Arjona T, Zhu JK.
PLoS Genet. 2015 Jan 8;11(1):e1004905.

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