Zheng Xia

Assistant Professor

  • 2106 Citations
  • 16 h-Index
20132018
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Research Output 2013 2018

  • 2106 Citations
  • 16 h-Index
  • 24 Article
2018

3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk

Park, H. J., Ji, P., Kim, S., Xia, Z., Rodriguez, B., Li, L., Su, J., Chen, K., Masamha, C. P., Baillat, D., Fontes-Garfias, C. R., Shyu, A. B., Neilson, J. R., Wagner, E. J. & Li, W. May 21 2018 (Accepted/In press) In : Nature Genetics. p. 1-7 7 p.

Research output: Contribution to journalArticle

3' Untranslated Regions
Tumor Suppressor Genes
Proto-Oncogenes
MicroRNAs
Neoplasms
2017
2 Citations

Aberrant plasticity of peripheral sensory axons in a painful neuropathy

Hirai, T., Mulpuri, Y., Cheng, Y., Xia, Z., Li, W., Ruangsri, S., Spigelman, I. & Nishimura, I. Dec 1 2017 In : Scientific Reports. 7, 1, 3407

Research output: Contribution to journalArticle

Axons
Messenger RNA
3' Untranslated Regions
Nerve Compression Syndromes
Polyadenylation
55 Citations

Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma

Ally, A. , Balasundaram, M. , Carlsen, R. , Chuah, E. , Clarke, A. , Dhalla, N. , Holt, R. A. , Jones, S. J. M. , Lee, D. , Ma, Y. , Marra, M. A. , Mayo, M. , Moore, R. A. , Mungall, A. J. , Schein, J. E. , Sipahimalani, P. , Tam, A. , Thiessen, N. , Cheung, D. , Wong, T. & 31 others Brooks, D., Robertson, A. G., Bowlby, R., Mungall, K., Sadeghi, S., Xi, L., Covington, K., Shinbrot, E., Wheeler, D. A., Gibbs, R. A., Donehower, L. A., Wang, L., Bowen, J., Gastier-Foster, J. M., Gerken, M., Helsel, C., Leraas, K. M., Lichtenberg, T. M., Ramirez, N. C., Wise, L., Zmuda, E., Gabriel, S. B., Meyerson, M., Cibulskis, C., Murray, B. A., Shih, J., Beroukhim, R., Cherniack, A. D., Mills, G. B., Xia, Z. & The Cancer Genome Atlas Research Network Jun 15 2017 In : Cell. 169, 7, p. 1327-1341.e23

Research output: Contribution to journalArticle

Hepatocellular Carcinoma
Genes
DNA
MicroRNAs
Gene expression
3 Citations

Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions

Brinegar, A. E., Xia, Z., Loehr, J. A., Li, W., Rodney, G. G. & Cooper, T. A. Aug 11 2017 In : eLife. 6, e27192

Research output: Contribution to journalArticle

Muscle Development
Calcineurin
Alternative Splicing
Muscle
Skeletal Muscle
5 Citations

Gleason score 7 prostate cancers emerge through branched evolution of clonal Gleason pattern 3 and 4

Sowalsky, A. G., Kissick, H. T., Gerrin, S. J., Schaefer, R. J., Xia, Z., Russo, J. W., Arredouani, M. S., Bubley, G. J., Sanda, M. G., Li, W., Ye, H. & Balk, S. P. Jul 15 2017 In : Clinical Cancer Research. 23, 14, p. 3823-3833 11 p.

Research output: Contribution to journalArticle

Clonal Evolution
Neoplasm Grading
Prostatic Neoplasms
Neoplasms
Gene Expression Profiling
3 Citations

Human mutations in integrator complex subunits link transcriptome integrity to brain development

Oegema, R. , Baillat, D. , Schot, R. , van Unen, L. M. , Brooks, A. , Kia, S. K. , Hoogeboom, A. J. M. , Xia, Z. , Li, W. , Cesaroni, M. , Lequin, M. H. , van Slegtenhorst, M. , Dobyns, W. B. , de Coo, I. F. M. , Verheijen, F. W. , Kremer, A. , van der Spek, P. J. , Heijsman, D. , Wagner, E. J. , Fornerod, M. & 1 others Mancini, G. M. S. May 1 2017 In : PLoS Genetics. 13, 5, e1006809

Research output: Contribution to journalArticle

Transcriptome
transcriptome
brain
mutation
Mutation
4 Citations

Poly(A)-ClickSeq: Click-chemistry for next-generation 3'-end sequencing without RNA enrichment or fragmentation

Routh, A., Ji, P., Jaworski, E., Xia, Z., Li, W. & Wagner, E. J. Jul 1 2017 In : Nucleic Acids Research. 45, 12, e112

Research output: Contribution to journalArticle

Click Chemistry
RNA Sequence Analysis
Poly A
Polyadenylation
RNA
2016
5 Citations

CFIm25 regulates glutaminase alternative terminal exon definition to modulate MIR-23 function

Masamha, C. P., Xia, Z., Peart, N., Collum, S., Li, W., Wagner, E. J. & Shyu, A. B. Jun 1 2016 In : RNA. 22, 6, p. 830-838 9 p.

Research output: Contribution to journalArticle

Glutaminase
3' Untranslated Regions
Exons
MicroRNAs
Polyadenylation
3 Citations

Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1

Giudice, J., Xia, Z., Li, W. & Cooper, T. A. Oct 19 2016 In : Scientific Reports. 6, 35550

Research output: Contribution to journalArticle

cdc Genes
RNA Stability
Transcriptome
Binding Sites
RNA Sequence Analysis
2015
49 Citations

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

Chen, K., Chen, Z., Wu, D., Zhang, L., Lin, X., Su, J., Rodriguez, B., Xi, Y., Xia, Z., Chen, X., Shi, X., Wang, Q. & Li, W. Sep 29 2015 In : Nature Genetics. 47, 10, p. 1149-1157 9 p.

Research output: Contribution to journalArticle

Tumor Suppressor Genes
Epigenomics
Neoplasms
Mutation
Genes
40 Citations

Long non-coding RNAs control hematopoietic stem cell function

Luo, M., Jeong, M., Sun, D., Park, H. J., Rodriguez, B. A. T., Xia, Z., Yang, L., Zhang, X., Sheng, K., Darlington, G. J., Li, W. & Goodell, M. A. Apr 2 2015 In : Cell Stem Cell. 16, 4, p. 426-438 13 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Hematopoietic Stem Cells
Binding Sites
Gene Expression
High-Throughput Nucleotide Sequencing
22 Citations

Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming

Hirsch, C. L. , Akdemir, Z. C. , Wang, L. , Jayakumaran, G. , Trcka, D. , Weiss, A. , Javier Hernandez, J. , Pan, Q. , Han, H. , Xu, X. , Xia, Z. , Salinger, A. P. , Wilson, M. , Vizeacoumar, F. , Datti, A. , Li, W. , Cooney, A. J. , Barton, M. C. , Blencowe, B. J. , Wrana, J. L. & 1 others Dent, S. Y. R. 2015 In : Genes and Development. 29, 8, p. 803-816 14 p.

Research output: Contribution to journalArticle

Alternative Splicing
Epigenomics
Histone Acetyltransferases
Gene Regulatory Networks
Embryonic Stem Cells
59 Citations

PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145

Yang, Y., Hadjikyriacou, A., Xia, Z., Gayatri, S., Kim, D., Zurita-Lopez, C., Kelly, R., Guo, A., Li, W., Clarke, S. G. & Bedford, M. T. Mar 4 2015 In : Nature Communications. 6, 6428

Research output: Contribution to journalArticle

Phosphatidyl-N-Methylethanolamine N-Methyltransferase
splicing
Arginine
methylation
proteins
41 Citations

Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer

Sowalsky, A. G., Xia, Z., Wang, L., Zhao, H., Chen, S., Bubley, G. J., Balk, S. P. & Li, W. Jan 1 2015 In : Molecular Cancer Research. 13, 1, p. 98-106 9 p.

Research output: Contribution to journalArticle

Castration
Transcriptome
Prostatic Neoplasms
Messenger RNA
RNA
2014
51 Citations

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development

Giudice, J., Xia, Z., Wang, E. T., Scavuzzo, M. A., Ward, A. J., Kalsotra, A., Wang, W., Wehrens, X. H. T., Burge, C. B., Li, W. & Cooper, T. A. Apr 22 2014 In : Nature Communications. 5, 3603

Research output: Contribution to journalArticle

splicing
Alternative Splicing
Cardiac Myocytes
genes
Genes
87 Citations

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

Masamha, C. P., Xia, Z., Yang, J., Albrecht, T. R., Li, M., Shyu, A. B., Li, W. & Wagner, E. J. 2014 In : Nature. 510, 7505, p. 412-416 5 p.

Research output: Contribution to journalArticle

Polyadenylation
Glioblastoma
3' Untranslated Regions
Neoplasms
RNA 3' End Processing
89 Citations

Dnmt3a and Dnmt3b have overlapping and distinct functions in hematopoietic stem cells

Challen, G. A., Sun, D., Mayle, A., Jeong, M., Luo, M., Rodriguez, B., Mallaney, C., Celik, H., Yang, L., Xia, Z., Cullen, S., Berg, J., Zheng, Y., Darlington, G. J., Li, W. & Goodell, M. A. 2014 In : Cell Stem Cell. 15, 3, p. 350-364 15 p.

Research output: Contribution to journalArticle

Hematopoietic Stem Cells
Null Lymphocytes
CpG Islands
Adult Stem Cells
Methyltransferases
62 Citations

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'2-UTR landscape across seven tumour types

Xia, Z., Donehower, L. A., Cooper, T. A., Neilson, J. R., Wheeler, D. A., Wagner, E. J. & Li, W. 2014 In : Nature Communications. 5, 5274

Research output: Contribution to journalArticle

Untranslated Regions
Polyadenylation
3' Untranslated Regions
Tumors
tumors
149 Citations

Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal

Sun, D., Luo, M., Jeong, M., Rodriguez, B., Xia, Z., Hannah, R., Wang, H., Le, T., Faull, K. F., Chen, R., Gu, H., Bock, C., Meissner, A., Göttgens, B., Darlington, G. J., Li, W. & Goodell, M. A. May 1 2014 In : Cell Stem Cell. 14, 5, p. 673-688 16 p.

Research output: Contribution to journalArticle

Hematopoietic Stem Cells
Epigenomics
Cell Aging
rRNA Genes
Genes
70 Citations

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

Hu, Z., Chen, K., Xia, Z., Chavez, M., Pal, S., Seol, J. H., Chen, C. C., Li, W. & Tyler, J. K. Feb 15 2014 In : Genes and Development. 28, 4, p. 396-408 13 p.

Research output: Contribution to journalArticle

Nucleosomes
Genomic Instability
Up-Regulation
Yeasts
Histones
34 Citations

Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis

Singh, R. K., Xia, Z., Bland, C. S., Kalsotra, A., Scavuzzo, M. A., Curk, T., Ule, J., Li, W. & Cooper, T. A. Aug 21 2014 In : Molecular Cell. 55, 4, p. 592-603 12 p.

Research output: Contribution to journalArticle

Muscle Development
Myoblasts
Alternative Splicing
Protein Isoforms
RNA-Binding Proteins
45 Citations

The histone-H3K4-specific demethylase KDM5B Binds to its substrate and product through distinct PHD fingers

Klein, B. J., Piao, L., Xi, Y., Rincon-Arano, H., Rothbart, S. B., Peng, D., Wen, H., Larson, C., Zhang, X., Zheng, X., Cortazar, M. A., Peña, P. V., Mangan, A., Bentley, D. L., Strahl, B. D., Groudine, M., Li, W., Shi, X. & Kutateladze, T. G. 2014 In : Cell Reports. 6, 2, p. 325-335 11 p.

Research output: Contribution to journalArticle

Histones
Fingers
Genes
Triple Negative Breast Neoplasms
Mi-2 Nucleosome Remodeling and Deacetylase Complex
95 Citations

ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression

Wen, H., Li, Y., Xi, Y., Jiang, S., Stratton, S., Peng, D., Tanaka, K., Ren, Y., Xia, Z., Wu, J., Li, B., Barton, M. C., Li, W., Li, H. & Shi, X. Apr 10 2014 In : Nature. 508, 7495, p. 263-268 6 p.

Research output: Contribution to journalArticle

Histones
RNA Polymerase II
Neoplasms
Chromatin
Genes
2013
1133 Citations

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N. , Collisson, E. A. , Mills, G. B. , Shaw, K. R. M. , Ozenberger, B. A. , Ellrott, K. , Sander, C. , Stuart, J. M. , Chang, K. , Creighton, C. J. , Davis, C. , Donehower, L. , Drummond, J. , Wheeler, D. , Ally, A. , Balasundaram, M. , Birol, I. , Butterfield, Y. S. N. , Chu, A. , Chuah, E. & 316 others Chun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T. Oct 2013 In : Nature Genetics. 45, 10, p. 1113-1120 8 p.

Research output: Contribution to journalArticle

Atlases
Genome
Neoplasms
Epigenomics
RNA