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Publications

  • 2023 Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou. 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. NATURE STRUCTURAL AND MOLECULAR BIOLOGY- doi: 10.1038/s41594-023-01130-4. PDF link

  • 2022    Di Giammartino DC, Polyzos A, Apostolou E. Assessing specific networks of chromatin interactions with HiChIP. Invited chapter for METHODS IN MOLECULAR BIOLOGY - Spatial Genome Organization special issue 2532:113-141 

  • 2021    Doane AS, Jiang Y, Di Giammartino DC, Helmut J, Rivas M, Yusova N, Chu CS, Alonso A, Apostolou E, Melnick M, Elemento O. OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. NATURE IMMUNOLOGY 10:1327-1340 PDF link

 

  • 2021    Pelham-Webb B, Polyzos A, Wojenski L, Kloetgen A, Li J, Di Giammartino DC, Core L, Tsirigos A and Apostolou E.  H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin organization. MOLECULAR CELL 81:1732-1748 PDF link

  • 2020    Di Giammartino DC, Polyzos A, Apostolou E. Transcription factors: building hubs in the 3D space. CELL CYCLE 12:1-16 PDF link

 

  • 2019    Lhoumaud P, Sethia G, Izzo F, Sakellaropoulos T, Snetkova V, Vidal S, Badri S, Cornwell M,  Di Giammartino DC, Kim K, Apostolou E, Stadtfeld M, Landau D, Skok J. EpiMethylTag simultaneously detects ATAC-seq or ChIP-seq signals with DNA methylation. GENOME BIOLOGY 20:248-260 PDF link

 

  • 2019    Di Giammartino DC*, Kloetgen A*, PolyzosA*, Liu Y, Kim D, Murphy D, Abuhashem A, Cavaliere P, Aronson B, Shah V, Dephoure N, Stadtfeld M, Tsirigos A, Apostolou E. KLF4 is involved in the organization and regulation of pluripotency-associated 3D enhancer networks.  NATURE CELL BIOLOGY 21:1179-1190 PDF link

  • 2019    Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. TAF5L and TAF6L maintain self-renewal of embryonic stem cells via the MYC regulatory network.  MOLECULAR CELL74:1148-1163 PDF link

  • 2017    Liu Y*, Pelham-Webb B*, Di Giammartino DC *, Li J, Kim D, Kita K, Saiz N, Garg V, Doane A, Giannakakou P, Hadjantonakis AK, Elemento O, Apostolou E. Widespread mitotic bookmarking by histone marks and transcription factors in pluripotent stem cells. CELL REPORTS 19:1283-93 (*equal contribution) PDF link

 

  • 2016    Di Giammartino DC, Apostolou E. The chromatin signature of pluripotency: establishment and maintenance. CURRENT STEM CELL REPORT 2:255-62 PDF link

  • 2014    Di Giammartino D.C., Li W., Yashinskie J., Tian B., Manley J.L. RBBP6 is a human polyadenylation factor that regulates mRNAs with AU-rich 3’UTRs. GENES & DEVELOPMENT 28:2248-60 PDF link

 

  • 2013    Di Giammartino D.C., Shi Y, Manley J.L. PARP1 represses PAP and inhibits polyadenylation during heat shock. MOLECULAR CELL 49:7-17 PDF link

 

  • 2013    Manley J.L., Di Giammartino D.C. mRNA polyadenylation in eukaryotes. ENCYCLOPEDIA OF BIOLOGICAL CHEMISTRY, Second edition, Elsevier (p.188-193)

 

  • 2013    Chan A.L., Grossman T., Zuckerman V., Campigli Di Giammartino D., Moshel O., Scheffner M., Monahan B., Pilling P., Jiang Y.H., Haupt S., Schueler-Furman O., Haupt Y. c-Abl phosphorylates E6AP and regulates its E3 ubiquitin ligase activity. BIOCHEMISTRY 52:3119-29 PDF link

 

  • 2011    Di Giammartino D.C., Nishida K., Manley J.L. Mechanisms and consequences of alternative polyadenylation. MOLECULAR CELL 43:853-66 PDF link

 

  • 2011    Shi Y., Nishida K., Campigli Di Giammartino D., Manley J.L.  Heat shock-induced SRSF10 dephosphorylation displays thermotolerance mediated by Hsp27. MOLECULAR AND CELLULAR BIOLOGY 31:458-65 PDF link

 

  • 2009    Shi Y., Di Giammartino D.C., Taylor D., Sharkeshik A., Rice W.J., Yates JR 3rd, Frank J., Manley J.L.  Molecular architecture of the human pre-mRNA 3’ processing complex. MOLECULAR CELL 33:365-7 PDF link

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