Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis

PhDEraRepresentativeRNA Splicing + RBPs
Albert W Cheng*, Jiahai Shi*, Piu Wong*, Katherine L Luo, Paula Trepman, Eric T Wang, Heejo Choi, Christopher B Burge, Harvey F Lodish
Blood 124(4):598-610
Publication year: 2014

Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state

Cancer + MetastasisPhDEraRNA Splicing + RBPs
Katz Y, Li F, Lambert NJ, Sokol ES, Tam WL, Cheng AW, Airoldi EM, Lengner CJ, Gupta PB, Yu Z, Jaenisch R, Burge CB
Elife 3:e03915
Publication year: 2014

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

EpigeneticsPhDEraStem Cells + Reprogramming
Dawlaty, M.M, Breiling, A., Le, Thuc, Barrasa, M.I., Raddatz, G., Gao, Q., Powell, B.E., Cheng, A.W., Faull, K.F., Lyko, F., Jaenisch, R.#
Developmental Cell 29(1):102-111
Publication year: 2014

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

CRISPR/Cas + TALENPhDEra
Wu, X., Scott, D.A., Kriz, A.J., Chiu, A.C., Hsu, P.D., Dadon, D.B., Cheng, A.W., Trevino, A.E., Konermann, S., Chen, S., Jaenisch, R., Zhang, F., Sharp, P.A.#
Nature Biotechnology 32(7):670-676
Publication year: 2014

Genetic and Chemical Correction of Cholesterol Accumulation and Impaired Autophagy in Hepatic and Neural Cells Derived from Niemann-Pick Type C Patient-Specific iPS Cells

DiseasesPhDEra
Maetzel, D., Sarkar, S., Wang, H., Abi-Mosleh, L., Xu, P., Cheng, A.W., Gao, Q., Mitalipova, M. Jaenisch, R.#
Stem Cell Reports 2(6):866-880
Publication year: 2014

Tet1 is critical for neuronal activity-regulated gene expression and memory extinction

EpigeneticsPhDEra
Rudenko, A., Dawlaty, M.M., Seo, J., Cheng, A.W., Meng, J., Le, T., Faull, K.F., Jaenisch, R., Tsai, L.H.#
Neuron 79(6):1109-1122
Publication year: 2013

TALEN-mediated editing of the mouse Y chromosome

CRISPR/Cas + TALENPhDEraSynthetic Biology + Genome Engineering
Wang, H.*, Hu, Y.C.*, Markoulaki, S., Welstead, C.G., Cheng, A.W., Shivalila, C.S., Pyntikova, T., Dadon, D.B., Voytas, D.F., Bogdanove, A.J., Page, D.C., Jaenisch, R.#
Nature Biotechnology 31(6):530-532
Publication year: 2013

SOX2 Co-occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

PhDEraStem Cells + Reprogramming
Lodato, M.A., Ng, C.W.*, Wamstad, J.A.*, Cheng, A.W., Thai, K.K., Faenkel, E., Jaenisch, R., Boyer, L.A.#
PLoS Genetics 9(2):e1003288
Publication year: 2013

Single-cell analysis reveals that expression of nanog is biallelic and equally variable as that of other pluripotency factors in mouse ESCs

PhDEraStem Cells + Reprogramming
Faddah, D.A., Wang, H., Cheng, A.W., Katz, Y., Buganim, Y., Jaenisch, R.#
Cell Stem Cell 13(1):23-29
Publication year: 2013

One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering

CRISPR/Cas + TALENPhDEra
Yang, H.*, Wang, H.*, Shivalila, C.S.*, Cheng, A.W., Shi, L., Jaenisch, R.#
Cell 154(6):1370-1379
Publication year: 2013

One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering

CRISPR/Cas + TALENPhDEra
Wang, H.*, Yang, H.*, Shivalila, C.S.*, Dawlaty, M.M., Cheng, A.W., Zhang, F., Jaenisch, R#
Cell 153(4):910-918
Publication year: 2013

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

CRISPR/Cas + TALENPhDEraRepresentativeSynthetic Biology + Genome Engineering
Albert W Cheng*, Haoyi Wang*, Hui Yang, Linyu Shi, Yarden Katz, Thorold W Theunissen, Sudharshan Rangarajan, Chikdu S Shivalila, Daniel B Dadon, Rudolf Jaenisch
Cell Research (2013) 23:1163-1171
Publication year: 2013

Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett Syndrome neurons

EpigeneticsPhDEra
Li, Y., Wang, H., Muffat, J., Cheng, A.W., Orlando, D.A., Loven, J., Kwok, S., Feldman, D.A., Bateup, H.S., Gao, Q., Hockemeyer, D., Mitalipova, M., Lewis, C.A., Heiden, W.G.V., Sur, M., Young, R.A., Jaenisch, R.#
Cell Stem Cell 13(4):446-458
Publication year: 2013

Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development

EpigeneticsPhDEraStem Cells + Reprogramming
Dawlaty, M.M., Breiling, A., Le, T., Raddatz, G., Barrasa, M.I., Cheng, A.W., Gao, Q., Powell, B.E., Li, Z., Xu, M., Faull, K.F., Lyko, F., Jaenisch R.#
Developmental Cell 24(3):310-323
Publication year: 2013

X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner

EpigeneticsPhDEraStem Cells + Reprogramming
Welstead, G.G., Creyghton, M.P., Bilodeau, S., Cheng, A.W., Markoulaki, S., Young, R.A., Jaenisch R.#
PNAS 109(32):13004-13009
Publication year: 2012

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase.

PhDEraRepresentativeStem Cells + Reprogramming
Buganim, Y.*, Faddah D.A.*, Cheng, A.W., Itskovich, E., Markoulaki, S., Gantz, K., Klemm S.L., van Oudenaarden A., Jaenisch, R.#
Cell 150(6):1209-1222
Publication year: 2012

Direct Reprogramming of Fibroblasts into Embryonic Sertoli-like Cells by Defined Factors

PhDEraStem Cells + Reprogramming
Buganim, Y., Itskovich, E., Hu, Y.-C., Cheng, A.W., Ganz, K., Sarkar, S., Fu, D.D., Welstead, G., Page, D.C., Jaenisch, R.#
Cell Stem Cell 11(3):373-386
Publication year: 2012

Alternatively spliced mRNA isoforms as prognostic indicators for metastatic cancer

Cancer + MetastasisPatentsPhDEraRepresentativeRNA Splicing + RBPs
Christopher Boyce BURGE, Wu Albert CHENG, John S. Condeelis, Frank B. Gertler, Maja H. OKTAY, Irina M. SHAPIRO
WO2012116248 A1
Publication year: 2012

Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development

EpigeneticsPhDEra
Dawlaty, M.M., Ganz, K., Powell, B.E., Hu, Y.C., Markoulaki, S., Cheng, A.W., Gao, Q., Kim, J., Choi, S.W., Page, D.C., Jaenisch, R.#
Cell Stem Cell 9(2):166-175
Publication year: 2011

Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations

PhDEraStem Cells + Reprogramming
Soldner, F., Laganière, J., Cheng, A.W., Hockemeyer, D., Gao, Q., Alagappan, R., Khurana, V., Golbe, L.I., Myers, R.H., Lindquist, S., Zhang, L., Guschin, D., Fong, L.K., Vu, B.J., Meng, X., Urnov, F.D., Rebar, E.J., Gregory, P.D., Zhang, H.S., Jaenisch, R.#
Cell 146(2):318-331
Publication year: 2011

Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes

EpigeneticsPhDEra
Wong, P., Hattangadi, S.M., Cheng, A.W., Frampton, G.M., Young, R.A., Lodish, H.F.#
Blood 118(16):E128-E138
Publication year: 2011

Functional integration of dopaminergic neurons directly converted from mouse fibroblasts

DiseasesPhDEraStem Cells + Reprogramming
Kim, J., Su, S.C., Wang, H., Cheng, A.W., Cassady, J.P., Lodato, M.A., Lengner, C.J., Chung, C.Y., Dawlaty, M.M., Tsai, L.H., Jaenisch R.#
Cell Stem Cell 9(5):413-419
Publication year: 2011

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

EpigeneticsPhDEraStem Cells + Reprogramming
Hanna J., Cheng, A.W., Saha K., Kim J.P., Lengner, C.J., Soldner, F., Cassady, J.P., Muffat, J., Carey, B.W., Jaenisch R.#
PNAS 107(20):9222-9227
Publication year: 2010

Histone H3K27ac separates active from poised enhancers and predicts developmental state

EpigeneticsPhDEraRepresentative
Menno P Creyghton*, Albert W Cheng*, G Grant Welstead, Tristan Kooistra, Bryce W Carey, Eveline J Steine, Jacob Hanna, Michael A Lodato, Garrett M Frampton, Phillip A Sharp, Laurie A Boyer, Richard A Young, Rudolf Jaenisch
PNAS 107(50):21931–21936
Publication year: 2010

Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations

PhDEraStem Cells + Reprogramming
Lengner C.J., Erwin, J.A.*, Gimelbrant A.A.*, Cheng A.W., Guenther M.G., Welstead G.G., Alagappan R., Frampton M.F., Xu P., Powers D., Barrett C.B., Young R.A., Lee J.T., Jaenisch R.#, Mitalipova, M.#
Cell 141(5):872-883
Publication year: 2010

An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

Cancer + MetastasisPhDEraRepresentativeRNA Splicing + RBPs
Irina M. Shapiro*, Albert W. Cheng*, Nicholas C. Flytzanis, Michele Balsamo, John S. Condeelis, Maja H. Oktay, Christopher B. Burge , Frank B. Gertler
PLoS Genet 7(8): e1002218
Publication year: 2010

Metastable Pluripotent States in NOD-Mouse-Derived ESCs

PhDEraStem Cells + Reprogramming
Hanna, J.*, Markoulaki, S.*, Mitalipova, M., Cheng, A.W., Cassady, J.P., Staerk, J., Carey, B.W., Lengner, C.J., Foreman, R., Love, J., Gao, Q., Kim, J., Jaenisch, R.#
Cell Stem Cell 4(6):513-524
Publication year: 2009

Transgenic mice with defined combinations of drug-inducible reprogramming factors

PhDEraStem Cells + Reprogramming
Markoulaki, S.*, Hanna, J.*, Beard, C., Carey, B.W., Cheng, A.W., Lengner, C.J., Dausman, J.A., Fu, D., Gao, Q., Wu, S., Cassady, J.P. and Jaenisch, R.#
Nature Biotechnology 27(2):169-171
Publication year: 2008