Selected Published Papers

2021

OBF1 and Oct factors control the germinal center transcriptional program

Song S, Cao C, Choukrallah MA, Tang F, Christofori G, Kohler H, Wu F, Fodor BD, Frederiksen M, Willis SN, Jackson JT, Nutt SL, Dirnhofer S, Stadler MB, Matthias P.
Blood. 2021 May 27;137(21):2920-2934. doi: 10.1182/blood.2020010175.

Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase

Liu W, Gallego-Bartolomé J, Zhou Y, Zhong Z, Wang M, Wongpalee SP, Gardiner J, Feng S, Kuo PH, Jacobsen SE.

Nat Commun. 2021 May 25;12(1):3130. doi: 10.1038/s41467-021-23346-y.

Initiation and amplification of SnRK2 activation in abscisic acid signaling

Lin Z, Li Y, Wang Y, Liu X, Ma L, Zhang Z, Mu C, Zhang Y, Peng L, Xie S, Song CP, Shi H, Zhu JK, Wang P.
Nat Commun. 2021 Apr 28;12(1):2456. doi: 10.1038/s41467-021-22812-x.
 

RNA Dysregulation: An Expanding Source of Cancer Immunotherapy Targets

Pan Y, Kadash-Edmondson KE, Wang R, Phillips J, Liu S, Ribas A, Aplenc R, Witte ON, Xing Y.
Trends Pharmacol Sci. 2021 Apr;42(4):268-282. doi: 10.1016/j.tips.2021.01.006.

Whole-genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth

Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L.
Plant J. 2021 Apr;106(2):435-453. doi: 10.1111/tpj.15174.

Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

Park CY, Zhou J, Wong AK, Chen KM, Theesfeld CL, Darnell RB, Troyanskaya OG.
Nat Genet. 2021 Jan 18. doi: 10.1038/s41588-020-00761-3.

Simultaneous Zn2+ tracking in multiple organelles using super-resolution morphology-correlated organelle identification in living cells

Fang H, Geng S, Hao M, Chen Q, Liu M, Liu C, Tian Z, Wang C, Takebe T, Guan JL, Chen Y, Guo Z, He W, Diao J.
Nat Commun. 2021 Jan 4;12(1):109. doi: 10.1038/s41467-020-20309-7.

Spatiotemporal analysis of human intestinal development at single-cell resolution

Fawkner-Corbett D, Antanaviciute A, Parikh K, Jagielowicz M, Gerós AS, Gupta T, Ashley N, Khamis D, Fowler D, Morrissey E, Cunningham C, Johnson PRV, Koohy H, Simmons A.
Cell. 2021 Jan 4:S0092-8674(20)31686-X. doi: 10.1016/j.cell.2020.12.016.


2020

RNA nucleation by MSL2 induces selective X chromosome compartmentalization

Valsecchi CIK, Basilicata MF, Georgiev P, Gaub A, Seyfferth J, Kulkarni T, Panhale A, Semplicio G, Manjunath V, Holz H, Dasmeh P, Akhtar A
Nature. 2020 Nov 18. doi: 10.1038/s41586-020-2935-z.

Spatiotemporal Proteomic Analysis of Stress Granule Disassembly Using APEX Reveals Regulation by SUMOylation and Links to ALS Pathogenesis

Marmor-Kollet H, Siany A, Kedersha N, … Ivanov P, Geiger T, Hornstein E
Mol Cell. 2020 Nov 19. DOI:https://doi.org/10.1016/j.molcel.2020.10.032

SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses

Banerjee AK, Blanco MR, Bruce EA, … Guttman M
Cell. 2020 Oct 8. DOI:https://doi.org/10.1016/j.cell.2020.10.004

Calcium modulates the domain flexibility and function of an α-actinin similar to the ancestral α-actinin

Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner C, Salmazo A, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro EA Jr, Marlovits TC, Bhattacharya A, Djinovic-Carugo K
Proc Natl Acad Sci U S A. 2020 Sep 8;117(36):22101-22112. doi: 10.1073/pnas.1917269117. Epub 2020 Aug 26.

A tumor-associated splice-isoform of MAP2K7 drives dedifferentiation in MBNL1-low cancers via JNK activation

Ray D, Yun YC, Idris M, Cheng S, Boot A, Iain TBH, Rozen SG, Tan P, Epstein DM.
Proc Natl Acad Sci U S A. 2020 Jul 14;117(28):16391-16400. doi: 10.1073/pnas.2002499117.

Acute Inhibition of Centriolar Satellite Function and Positioning Reveals their Functions at the Primary Cilium

Aydin OZ, Taflan SO, Gurkaslar C, Firat-Karalar E
PLoS Biology 2020 June 18. doi: 10.1371/journal.pbio.3000679.

AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2

Yang A, Shao TJ, Bofill-De Ros X, Lian C, Villanueva P, Dai L,Gu S.

Nat Commun. 2020 Jun 2;11(1):2765. doi: 10.1038/s41467-020-16533-w.

A slipped-CAG DNA-binding Small Molecule Induces Trinucleotide-Repeat Contractions in Vivo

Nakamori M, Panigrahi GB, Lanni S, Gall-Duncan T, Hayakawa H, Tanaka H, Luo J, Otabe T, Li J, Sakata A, Caron MC, Joshi N, Prasolava T, Chiang K, Masson JY, Wold MS, Wang X, Lee MYWT, Huddleston J, Munson KM, Davidson S, Layeghifard M, Edward LM, Gallon R, Santibanez-Koref M, Murata A, Takahashi MP, Eichler EE, Shlien A, Nakatani K, Mochizuki H, Pearson CE.
Nat Genet. 2020 Feb 14. doi: 10.1038/s41588-019-0575-8.

A RAF-SnRK2 kinase cascade mediates early osmotic stress signaling in higher plants

Lin Z, Li Y, Zhang Z, Liu X, Hsu CC, Du Y, Sang T, Zhu C, Wang Y, Satheesh V, Pratibha P, Zhao Y, Song CP, Tao WA, Zhu JK,Wang P
Nat Commun. 2020 Jan 30;11(1):613. doi: 10.1038/s41467-020-14477-9.

Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks

Zhu H, Uusküla-Reimand L, Isaev K, Wadi L, Alizada A, Shuai S, Huang V, Aduluso-Nwaobasi D, Paczkowska M, Abd-Rabbo D, Ocsenas O, Liang M, Thompson JD, Li Y, Ruan L, Krassowski M, Dzneladze I, Simpson JT, Lupien M, Stein LD, Boutros PC, Wilson MD, Reimand J.
Mol Cell. 2020 Jan 17. pii: S1097-2765(19)30957-8.


2019

Single-cell analysis uncovers that metabolic reprogramming by ErbB2 signaling is essential for cardiomyocyte proliferation in the regenerating heart.

Honkoop H, de Bakker DE, Aharonov A, Kruse F, Shakked A, Nguyen PD, de Heus C, Garric L, Muraro MJ, Shoffner A, Tessadori F, Peterson JC, Noort W, Bertozzi A, Weidinger G, Posthuma G, Grün D, van der Laarse WJ, Klumperman J, Jaspers RT, Poss KD, van Oudenaarden A, Tzahor E, Bakkers J.

Elife. 2019 Dec 23;8. pii: e50163.

The conical shape of DIM lipids promotes Mycobacterium tuberculosis infection of macrophages.

Augenstreich J, Haanappel E, Ferré G, Czaplicki G, Jolibois F, Destainville N, Guilhot C, Milon A, Astarie-Dequeker C, Chavent M.
Proc Natl Acad Sci U S A. 2019 Nov 22. pii: 201910368.

An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis.

Liu J, Feng L, Gu X, Deng X, Qiu Q, Li Q, Zhang Y, Wang M, Deng Y, Wang E, He Y, Bäurle I, Li J, Cao X, He Z.
Cell Res. 2019 May;29(5):379-390

Inheritance of a Phenotypically Neutral Epimutation Evokes Gene Silencing in Later Generations

Duempelmann L, Mohn F, Shimada Y, Oberti D, Andriollo A, Lochs S, Bühler M.
Mol Cell. 2019 May 2;74(3):534-541.

Oscillatory shear potentiates latent TGF-β1 activation more than steady shear as demonstrated by a novel force generator.

Kouzbari K, Hossan MR, Arrizabalaga JH, Varshney R, Simmons AD, Gostynska S, Nollert MU, Ahamed J.
Sci Rep. 2019 Apr 15;9(1):6065.

Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing.

Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O.
Nat Commun. 2019 Apr 29;10(1):1931.

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