Department of Cell Biology

Top Notch Papers


Human telomeres replicate using chromosome-specific, rather than universal, replication programs.
Drosopoulos WC, Kosiyatrakul ST, Yan Z, Calderano SG, Schildkraut CL. J Cell Biol. 2012 Apr 16;197(2):253-66.

Bax regulates primary necrosis through mitochondrial dynamics.
Whelan RS, Konstantinidis K, Wei AC, Chen Y, Reyna DE, Jha S, Yang Y, Calvert JW, Lindsten T, Thompson CB, Crow MT, Gavathiotis E, Dorn GW 2nd, O'Rourke B, Kitsis RN. Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6566-71.

Overexpression of IL-1 receptor accessory protein in stem and progenitor cells and outcome correlation in AML and MDS.
Barreyro L, Will B, Bartholdy B, Zhou L, Todorova TI, Stanley RF, Ben-Neriah S, Montagna C, Parekh S, Pellagatti A, Boultwood J, Paietta E, Ketterling RP, Cripe L, Fernandez HF, Greenberg PL, Tallman MS, Steidl C, Mitsiades CS, Verma A, Steidl U. Blood. 2012 Aug 9;120(6):1290-8.

H2.0-like homeobox regulates early hematopoiesis and promotes acute myeloid leukemia.
Kawahara M, Pandolfi A, Bartholdy B, Barreyro L, Will B, Roth M, Okoye-Okafor UC, Todorova TI, Figueroa ME, Melnick A, Mitsiades CS, Steidl U. Cancer Cell. 2012 Aug 14;22(2):194-208.

Adrenergic nerves govern circadian leukocyte recruitment to tissues.
Scheiermann C, Kunisaki Y, Lucas D, Chow A, Jang JE, Zhang D, Hashimoto D, Merad M, Frenette PS. Immunity. 2012 Aug 24;37(2):290-301.

β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration.
Katz ZB, Wells AL, Park HY, Wu B, Shenoy SM, Singer RH. Genes Dev. 2012 Sep 1;26(17):1885-90.

Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations.
Will B, Zhou L, Vogler TO, Ben-Neriah S, Schinke C, Tamari R, Yu Y, Bhagat TD, Bhattacharyya S, Barreyro L, Heuck C, Mo Y, Parekh S, McMahon C, Pellagatti A, Boultwood J, Montagna C, Silverman L, Maciejewski J, Greally JM, Ye BH, List AF, Steidl C, Steidl U, Verma A. Blood. 2012 Sep 6;120(10):2076-86.

A PML–PPAR-δ pathway for fatty acid oxidation regulates hematopoietic stem cell maintenance.
Ito K, Carracedo A, Weiss D, Arai F, Ala U, Avigan DE, Schafer ZT, Evans RM, Suda T, Lee CH, Pandolfi PP. Nat Med. 2012 Sep;18(9):1350-8.

Hydroxyurea and a cGMP-amplifying agent have immediate benefits on acute vaso-occlusive events in sickle cell disease mice.
Almeida CB, Scheiermann C, Jang JE, Prophete C, Costa FF, Conran N, Frenette PS. Blood. 2012 Oct 4;120(14):2879-88.

IGHV unmutated and mutated chronic lymphocytic leukemia cells produce activation-induced deaminase protein with a full range of biologic functions.
Patten PE, Chu CC, Albesiano E, Damle RN, Yan XJ, Kim D, Zhang L, Magli AR, Barrientos J, Kolitz JE, Allen SL, Rai KR, Roa S, Mongini PK, Maccarthy T, Scharff MD, Chiorazzi N. Blood. 2012 Oct 15. [Epub ahead of print]

Zinc-finger nuclease-mediated correction of α-thalassemia in iPS cells.
Chang CJ, Bouhassira EE. Blood. 2012 Nov 8;120(19):3906-14.

The ATPase activity of MLH1 is required to orchestrate DNA double-strand breaks and end processing during class switch recombination. Chahwan R, van Oers JM, Avdievich E, Zhao C, Edelmann W, Scharff MD, Roa S. J Exp Med. 2012 April 9; 209(4):671-8. 

Identification and characterization of ToRC, a novel ISWI-containing ATP-dependent chromatin assembly complex. Emelyanov AV, Vershilova E, Ignatyeva MA, Pokrovsky DK, Lu X, Konev AY, Fyodorov DV. Genes Dev. 2012 Mar 15;26(6):603-14.

A core erythroid transcriptional network is repressed by a master regulator of myelo-lymphoid differentiation. Wontakal SN, Guo X, Smith C, Maccarthy T, Bresnick EH, Bergman A, Snyder MP, Weissman SM, Zheng D, Skoultchi AI. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3832-7. Epub 2012 Feb 22.

Slug and sox9 cooperatively determine the mammary stem cell state. Guo W, Keckesova Z, Donaher JL, Shibue T, Tischler V, Reinhardt F, Itzkovitz S, Noske A, Zürrer-Härdi U, Bell G, Tam WL, Mani SA, van Oudenaarden A, Weinberg RA. Cell. 2012 Mar 2;148(5):1015-28.

Norepinephrine reuptake inhibition promotes mobilization in mice: potential impact to rescue low stem cell yields. Lucas D, Bruns I, Battista M, Magnon C, Kunisaki Y, Frenette PS. Blood. 2012 Mar 14. [Epub ahead of print]

Enhanced outgrowth of EBV-transformed chronic lymphocytic leukemia B cells mediated by coculture with macrophage feeder cells. Hwang KK, Chen X, Kozink DM, Gustilo M, Marshall DJ, Whitesides JF, Liao HX, Catera R, Chu CC, Yan XJ, Luftig MA, Haynes BF, Chiorazzi N. Blood. 2012 Feb 16;119(7):e35-44. Epub 2011 Dec 12.



Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast. Trcek T, Larson DR, Moldón A, Query CC, Singer RH. Cell. 2011 Dec 23;147(7):1484-97.

A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1. Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI. PLoS Genet. 2011 Jun;7(6):e1001392.

CXCL1 and its receptor, CXCR2, mediate murine sickle cell vaso-occlusion during hemolytic transfusion reactions. Jang JE, Hod EA, Spitalnik SL, Frenette PS. J Clin Invest. 2011 Apr 1;121(4):1397-401. doi: 10.1172/JCI45336. 

Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Larson DR, Zenklusen D, Wu B, Chao JA, Singer RH. Science. 2011 Apr 22;332(6028):475-8. 

Bone marrow CD169+ macrophages promote the retention of hematopoietic stem and progenitor cells in the mesenchymal stem cell niche. Chow A, Lucas D, Hidalgo A, Méndez-Ferrer S, Hashimoto D, Scheiermann C, Battista M, Leboeuf M, Prophete C, van Rooijen N, Tanaka M, Merad M, Frenette PS. J Exp Med. 2011 Feb 14;208(2):261-71. 



Rewiring of genetic networks in response to DNA damage. Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Science. 2010 Dec 3;330(6009):1385-9.  

A testis-specific regulator of complex and hybrid N-glycan synthesis. Huang HH, Stanley P. J Cell Biol. 2010 Sep 6;190(5):893-910.  

In vivo imaging of labelled endogenous β-actin mRNA during nucleocytoplasmic transport. Grünwald D, Singer RH. Nature. 2010 Sep 30;467(7315):604-7.

Mesenchymal and haematopoietic stem cells form a unique bone marrow niche. Méndez-Ferrer S, Michurina TV, Ferraro F, Mazloom AR, Macarthur BD, Lira SA, Scadden DT, Ma'ayan A, Enikolopov GN, Frenette PS. Nature. 2010 Aug 12;466(7308):829-34.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance. van Oers JM, Roa S, Werling U, Liu Y, Genschel J, Hou H Jr, Sellers RS, Modrich P, Scharff MD, Edelmann W. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13384-9.

Requirement for cyclin D3 in germinal center formation and function. Peled JU, Yu JJ, Venkatesh J, Bi E, Ding BB, Krupski-Downs M, Shaknovich R, Sicinski P, Diamond B, Scharff MD, Ye BH. Cell Res. 2010 Jun;20(6):631-46.

Cis lethal genetic interactions attenuate and alter p53 tumorigenesis. Wang Y, Zhang W, Edelmann L, Kolodner RD, Kucherlapati R, Edelmann W. Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5511-5.



Predictable dynamic program of timing of DNA replication in human cells. Desprat R, Thierry Mieg D, Lailler N, Lajugie J, Schildkraut C, Thierry-Mieg J, Bouhassira EE. Genome Res. 2009 Dec;19(12):2288-99.

An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Kim HS, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bähler J, Keogh MC. Nat Struct Mol Biol. 2009 Dec;16(12):1286-93.

Decreased replication origin activity in temporal transition regions. Guan Z, Hughes CM, Kosiyatrakul S, Norio P, Sen R, Fiering S, Allis CD, Bouhassira EE, Schildkraut CL. J Cell Biol. 2009 Nov 30;187(5):623-35.

Effect of the nonpeptide thrombopoietin receptor agonist Eltrombopag on bone marrow cells from patients with acute myeloid leukemia and myelodysplastic syndrome. Will B, Kawahara M, Luciano JP, Bruns I, Parekh S, Erickson-Miller CL, Aivado MA, Verma A, Steidl U. Blood. 2009 Oct 29;114(18):3899-908.

V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence environment. MacCarthy T, Kalis SL, Roa S, Pham P, Goodman MF, Scharff MD, Bergman A. Proc Natl Acad Sci U S A. 2009 May 26;106(21):8629-34.

H3 trimethyl K9 and H3 acetyl K9 chromatin modifications are associated with class switch recombination. Kuang FL, Luo Z, Scharff MD. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5288-93. 

Linker histone H1 is essential for Drosophila development, the establishment of pericentric heterochromatin, and a normal polytene chromosome structure. Lu X, Wontakal SN, Emelyanov AV, Morcillo P, Konev AY, Fyodorov DV, Skoultchi AI. Genes Dev. 2009 Feb 15;23(4):452-65.

Insights into branch nucleophile positioning and activation from an orthogonal pre-mRNA splicing system in yeast. Smith, D.J., Konarska, M.M., and Query, C.C. Molecular Cell (2009) 34, 333–343.

Ubiquitylated PCNA plays a role in somatic hypermutation and class-switch recombination and is required for meiotic progression. Roa S, Avdievich E, Peled JU, Maccarthy T, Werling U, Kuang FL, Kan R, Zhao C, Bergman A, Cohen PE, Edelmann W, Scharff MD. Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16248-53. Epub 2008 Oct 14.



A stable prefusion intermediate of the alphavirus fusion protein reveals critical features of class II membrane fusion. Sánchez-San Martín C, Sosa H, Kielian M. Cell Host Microbe. 2008 Dec 11;4(6):600-8.

Single-RNA counting reveals alternative modes of gene expression in yeast. Zenklusen D, Larson DR, Singer RH. Nat Struct Mol Biol. 2008 Dec;15(12):1263-71. Epub 2008 Nov 16.

Globin switches in yolk sac-like primitive and fetal-like definitive red blood cells produced from human embryonic stem cells. Qiu C, Olivier EN, Velho M, Bouhassira EE. Blood. 2008 Feb 15;111(4):2400-8. Epub 2007 Nov 16.

The O-fucose glycan in the ligand-binding domain of Notch1 regulates embryogenesis and T cell development. Ge C, Stanley P. Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1539-44.

Constitutively activated STAT3 promotes cell proliferation and survival in the activated B-cell subtype of diffuse large B-cell lymphomas. Ding BB, Yu JJ, Yu RY, Mendez LM, Shaknovich R, Zhang Y, Cattoretti G, Ye BH. Blood.2008 Feb 1;111(3):1515-23.



Regulation of p53 tetramerization and nuclear export by ARC. Foo RS, Nam YJ, Ostreicher MJ, Metzl MD, Whelan RS, Peng CF, Ashton AW, Fu W, Mani K, Chin SF, Provenzano E, Ellis I, Figg N, Pinder S, Bennett MR, Caldas C, Kitsis RN. Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20826-31.

Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fidelity of spliceosome assembly. Xu, Y.-Z. and Query, C.C. Molecular Cell, 2007 838-849.

Structure of CD84 provides insight into SLAM family function. Yan Q, Malashkevich VN, Fedorov A, Fedorov E, Cao E, Lary JW, Cole JL, Nathenson SG, Almo SC. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10583-8.

Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation. Ronai D, Iglesias-Ussel MD, Fan M, Li Z, Martin A, Scharff MD. J Exp Med. 2007 Jan 22;204(1):181-90.

Global chromatin compaction limits the strength of the DNA damage response. Murga M, Jaco I, Fan Y, Soria R, Martinez-Pastor B, Cuadrado M, Yang SM, Blasco MA, Skoultchi AI, Fernandez-Capetillo O. J Cell Biol. 2007 Sep 24;178(7):1101-8.

CHD1 motor protein is required for deposition of histone variant H3.3 into chromatin in vivo.Konev AY, Tribus M, Park SY, Podhraski V, Lim CY, Emelyanov AV, Vershilova E, Pirrotta V, Kadonaga JT, Lusser A, Fyodorov DV.Science. 2007 Aug 24;317(5841):1087-90.

Opposing classes of prp8 alleles modulate the transition between the catalytic steps of pre-mRNA splicing. Liu L, Query CC, Konarska MM. Nat Struct Mol Biol. 2007 Jun;14(6):519-26. Epub 2007 May 7.



NTB-A Receptor Crystal Structure: Insights into Homophilic Interactions in the Signaling Lymphocytic Activation Molecule Receptor Family. Cao E, Ramagopal UA, Fedorov A, Fedorov E, Yan Q, Lary JW, Cole JL, Nathenson SG, Almo SC. Immunity. 2006 Oct;25(4):559-70.

The mismatch repair protein Msh6 influences the in vivo AID targeting to the Ig locus. Li Z, Zhao C, Iglesias-Ussel MD, Polonskaya Z, Zhuang M, Yang G, Luo Z, Edelmann W, Scharff MD. Immunity. 2006 Apr;24(4):393-403.

Repositioning of the reaction intermediate within the catalytic center of the spliceosome. Konarska MM, Vilardell J, Query CC. Mol Cell. 2006 Feb 17;21(4):543-53.


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