Neutralizing Gatad2a-Chd4-Mbd3 Axis within the NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

Mor N, Rais Y, Peles S, Sheban D, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E Lasman L, Shani T Bayerl J, Gafni O Hanna S Buenrostro J Hagai T Masika H Bergman Y Greenleaf WJ Esteban MA Levin YMassarwa R, Merbl Y Novershtern N &   Hanna JH


Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs

Mitsunaga S, Odajima J, Yawata S, Shioda K, Owa C,  Isselbacher KJ, Hanna  JH, Shioda T PNAS, Oct 2017

High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency

Zviran A, Mor N Rais Y, Gingold H, Peles S, Chomsky E, Viukov S, . Buenrostro JD, Weinberger L Manor YS Krupalnik V, Zerbib M, Hezroni H, Adhemar Jaitin D, Larastiaso D, Gilad S, Benjamin S Mousa A Ayyash M, Sheban D Bayerl J Aguilera Castrejon A Massarwa R, Maza I Hanna S, Amit I Stelzer Y Ulitsky I Greenleaf WJ Pilpel Y, Novershtern N Hanna JH Biorxiv, 2017

OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs

Sheinboim D,Maza I, Dror I, Parikh S, Krupalnik V, Bell RE , Zviran A, Suita Y, Mandel-Gutfreund Y, Khaled M, Hanna JH, Levy C Nature Communications 8, Oct 2017

Increased NK cell immunity in a transgenic mouse model of NKp46 overexpression

Glasner A,  Isaacson B, Viukov S, Neuman T, Friedman N,  Mandelboim M, Sexl V, Hanna JH, Mandelboim O

Scientific Reports 7, Oct 2017

A multiplexed screening method for pluripotency

Plotnikov A, Kozer N,  Krupalnik V,  Peles S, Mor N,  Rais Y,  Hanna JH, Barr HM Stem Cell Research 23, Aug 2017

m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

Ke S, Pandya-Jones A, Saito Y,  Fak JJ, Broberg Vågbø C , Geula S, Hanna JH, Black DL, Darnell JE Jr, Darnell RB

Genes and Development 31, May 2017

Transcriptional programs that control expression of the autoimmune regulator gene Aire

Herzig Y, Nevo S., Burnstein C., Brezis M., Ben-Hur S., Shkedy A., Eisenberge-Bord M, Levi B, Delacher M., Goldfarb Y., David E., Weinberger L. Viukov S., Ben-Dor S., Giraud M., Hanna JH, Breilling A., Lyko F., Amit I., Feuerer M & Abramson J.

Nature Immunology,  Feb 2017


Co-ChIP enables Genome-wide mapping of histone mark co-occurrence at single molecule resolution.

Weiner A, Lara-Astiaso D, Krupalnik V, Gafni O, David E, Winter D, Hanna JH & Amit I.  Nature Biotechnology, July 2016

Understanding Stem cell states: naïve to primed pluripotency in rodents and humans.

Leehee Weinberger, Muneef Ayyash, Noa Novershtern & Jacob H. Hanna.

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs.

Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Guttman M, Hanna JH, Regev A & Garber M. Genome Biology, Feb 2016

An essential role for UTX in resolution and activation of bivalent promoters.

Dhar SS, Lee S, Chen K, Zhu G, Oh K, Alton K, Gafni O, Kim YZ, Barton MC, Hanna JH, Wang Z, Li W & Lee MG.

Nucleic Acid Research, Jan 2016



Establishing the human naïve pluripotent state

Manor YS, Massarwa R, Hanna JH

Current Opinion in Genetics & Development, Oct 2015

Failure to replicate STAP cell phenomenon.

De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Tu H, Ross S, Doulatov S, Nguyen M, Wu Z, Theunissen T, Powell B, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin S, Park P and Daley GQ.

Nature, Sep 2015

Transient Acquisition of Pluripotency During Somatic Cell Trans-differentiation with iPSC Reprogramming Factors

Maza I, Caspi I, Zviran A, Chomsky E, Rais Y, Viukov S, Geula S, Buenrostro JD, Weinberger L, Krupalnik V, Hanna S., Zerbib M, Dutton JR, Greenleaf WJ, Massarwa R, Novershtern N & Hanna JH.

Nature Biotechnology, Jul 2015

Nature Methods Highlight

Poster: Stem cell states: naïve to primed pluripotency.

Leehee Weinberger, Yair S. Manor, Jacob H. Hanna.

Nature Rev Mol Cell Bio, Jun 2015

CD24 tracks divergent pluripotent states in mouse and human cells.

Shakiba N, White CA, Lipsitz YY, Yachie-Kinoshita A, Tonge PD, Hussein SM, Puri MC, Elbaz J, Morrissey-Scoot J, Li M, Munoz J, Benevento M, Rogers IM, Hanna JH, Heck AJ, Wollscheid B, Nagy A, Zandstra PW.

Nat Commun. Jun 2015

Lymphatic vessels arise from specialized angioblasts within a venous niche

J. Nicenboim*, G. Malkinson*, T. Lupo, L. Asaf, Y. Sela, O. Mayseless, L. Gibbs-Bar, N. Senderovich, T. Hashimshony, M. Shin, A. Jerafi-Vider, I. Avraham-Davidi, V. Krupalnik, R. Hofi, G. Almog, J. W. Astin, O. Golani, S. Ben-Dor, P. S. Crosier, W. Herzog, N. D. Lawson, J. H. Hanna, I. Yanai & K. Yaniv Nature, May 2015

Mbd3/NuRD is a Key Inhibitory Module During the Induction and Maintenance of Naïve Pluripotency

Asaf Zviran Yoach Rais Nofar Mor Noa Novershtern Jacob H Hanna

m6A mRNA Methylation Facilitates Resolution of Naïve Pluripotency Towards Differentiation.

Geula S.*, Moshitch-Moshkovitz S.*, Dominissini D.*, Mansour AA.*, Kol N., Salmon-Divon M., Hershkovitz V., Peer E., Mor N., Manor YS., Ben Haim M.S., Eyal E., Yunger S., Pinto Y., Jaitin DA., Viukov S., Rais Y., Krupalnik V., Chomsky E., Zerbib M., Maza I., Rechavi Y., Massarwa R., Hanna S., Ido Amit, Levanon EY., Amariglio N., Stern-Ginossar N., Novershtern N.#, Rechavi G.# and Hanna JH#.

(*Equal contribution, #Equal correspondence)

Science, Feb 2015

Perspective in Science 

Nature Chemical Biology Highlight

SOX17 is a Critical Specifier of Human Primordial Germ Cell Fate.

Irie N.*, Weinberger L.*, Tang W.*, Viukov S., Kobayashi T., Manor Y., Dietmann S., Hanna JH.# and Surani A#. (*Equal contribution, #Equal correspondence) Cell, Jan 2015 Nature highlight Nat Rev MCB highlight


Passage number is a major contributor to genomic structural variations in mouse iPSCs.

Liu P, Kaplan A, Yuan B, Hanna JH, Lupski JR, Reiner O.

Stem Cells, Oct 2014

Hijacked by an oocyte: hierarchical molecular changes in somatic cell nuclear transfer.

Stem cells: The quest for the perfect reprogrammed cell.

Krupalnik V, Hanna JH.

Nature, Jul 2014 (News & Views)

Lucky iPSCs

Asaf Zviran & Jacobv H Hanna

Genome Biology, Apr 2014 (Research Highlight)


Derivation of novel human ground state naive pluripotent stem cells

Ohad Gafni*, Leehee Weinberger*, Abed AlFatah Mansour*, Yair S. Manor*, Elad Chomsky*, Dalit Ben-Yosef, Yael Kalma, Sergey Viukov, Itay Maza, Asaf Zviran, Yoach Rais, Zohar Shipony, Zohar Mukamel, Vladislav Krupalnik, Mirie Zerbib, Shay Geula, Inbal Caspi, Dan Schneir, Tamar Shwartz, Shlomit Gilad, Daniela Amann-Zalcenstein, Sima Benjamin, Ido Amit, Amos Tanay, Rada Massarwa, Noa Novershtern & Jacob H. Hanna

Nature, Oct 2013

Nature Biotechnology highlight

Deterministic direct reprogramming of somatic cells to pluripotency

Yoach Rais*, Asaf Zviran*, Shay Geula*, Ohad Gafni, Elad Chomsky, Sergey Viukov, Abed AlFatah Mansour, Inbal Caspi, Vladislav Krupalnik, Mirie Zerbib, Itay Maza, Nofar Mor, Dror Baran, Leehee Weinberger, Diego A. Jaitin, David Lara-Astiaso, Ronnie Blecher-Gonen, Zohar Shipony, Zohar Mukamel, Tzachi Hagai, Shlomit Gilad, Daniela Amann-Zalcenstein, Amos Tanay, Ido Amit, Noa Novershtern & Jacob H. Hanna

Nature, Sep 2013

Nature Highlight

Science Highlight

News and Views, Nature 2013

The expression of the beta cell-derived autoimmune ligand for the killer receptor nkp46 is attenuated in type 2 diabetes.

Gur C, Enk J, Weitman E, Bachar E, Suissa Y, Cohen G, Schyr RB, Sabanay H, Horwitz E, Glaser B, Dor Y, Pribluda A, Hanna JH, Leibowitz G, Mandelboim O.

PLoS One, Aug 2013

Oct4 shuffles Sox partners to direct cell fate.


The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

Abed AlFatah Mansour*, Ohad Gafni*, Leehee Weinberger, Asaf Zviran, Muneef Ayyash, Yoach Rais, Vladislav Krupalnik, Mirie Zerbib, Daniela Amann-Zalcenstein, Itay Maza, Shay Geula, Sergey Viukov, Liad Holtzman, Ariel Pribluda, Eli Canaani, Shirley Horn-Saban, Ido Amit, Noa Novershtern* & Jacob H. Hanna

Nature, July 2012


RNF20 and USP44 Regulate Stem Cell Differentiation by Modulating H2B Monoubiquitylation.

Fuchs G, Shema E, Vesterman R, Kotler E, Wolchinsky Z, Wilder S, Golomb L, Pribluda A, Zhang F, Haj-Yahya M, Feldmesser E, Brik A, Yu X, Hanna J, Aberdam D, Domany E, Oren M.

Mol Cell Jun 2012

Tracing the genesis of human embryonic stem cells


esBAF safeguards Stat3 binding to maintain pluripotency

Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells.

Carey BW, Markoulaki S, Hanna JH, Faddah DA, Buganim Y, Kim J, Ganz K, Steine EJ, Cassady JP, Creyghton MP, Welstead GG, Gao Q, Jaenisch R.

Cell Stem Cell Dec 2011

Reprogramming of postnatal neurons into induced pluripotent stem cells by defined factors.

Kim J, Lengner CJ, Kirak O, Hanna J, Cassady JP, Lodato MA, Wu S, Faddah DA, Steine EJ, Gao Q, Fu D, Dawlaty M, Jaenisch R.

Stem Cells Jun 2011


Epigenetic Reprogramming of somatic and pluripotent cell states: Facts, Hypotheses and Unresolved issues.

Hanna J, Saha K & Jaenisch R.
Cell, Nov 2010

The STATs on naive iPSC reprogramming.

Epigenetic memory in induced pluripotent stem cells.

Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ.

Nature, Sep 2010

Reprogramming of human peripheral blood cells to induced pluripotent stem cells.

Staerk J, Dawlaty MM, Gao Q, Maetzel D, Hanna J, Sommer CA, Mostoslavsky G, Jaenisch R.

Cell Stem Cell,  Jul 2010

Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs.

Hanna J, Cheng AW, Saha K, Lengner CJ, Soldner F, Carey BW & Jaenisch R. 2010.
PNAS, Apr 2010

Single-gene transgenic mouse strains for reprogramming adult somatic cells.

Carey BW, Markoulaki S, Beard C, Hanna J, Jaenisch R.

Nat Methods, Jan 2010


Direct cell reprogramming is a stochastic process amenable to acceleration.

Hanna J, Saha K, Pando B, Lengner CJ, van Oudenaarden A & Jaenisch R.
Nature, Dec 2009

Metastable pluripotency states in NOD-mouse-derived ESCs.

Hanna J, Markoulaki S, Mitalipova M, Cheng AW, Carey BW, Lengner CJ, Love J,  & Jaenisch R.
Cell Stem Cell, July  2009

Transgenic mice with defined combinations of drug-inducible reprogramming factors

Markoulaki S*, Hanna J*, Carey BW, Beard C, Wu S., Lengner CJ, Dausman JA,  & Jaenisch R.
Nature Biotechnology, Feb 2009


H2AZ is enriched at polycomb complex target genes in ES cells and is necessary for lineage commitment.

Creyghton MP, Markoulaki S, Levine SS, Hanna J, Lodato MA, Sha K, Young RA, Jaenisch R, Boyer LA.

Cell, Nov 2008

Genome-scale DNA methylation maps of pluripotent and differentiated cells.

Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES.

Nature, Aug 2008

A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types.

Wernig M, Lengner CJ, Hanna J, Lodato MA, Steine E, Foreman R, Staerk J, Markoulaki S, Jaenisch R.

Nat Biotechnol, Aug 2008

Dissecting direct reprogramming through integrative genomic analysis.

Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A.

Nature, July 2008

Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency.

Hanna J, Markoulaki S, Schorderet P, Carey BW, Beard C, Wernig M, Creyghton MP, Steine EJ, Cassady JP, Foreman R, Lengner CJ, Dausman JA, & Jaenisch R.
Cell, Apr 2008


Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin.

Hanna J, Wernig M, Markoulaki S, Sun CW, Meissner A, Cassady J, Beard C, Wu LC, Brambrink T, Townes T, & Jaenisch R.
Science Dec 2007