Ivan D'Orso, Ph.D.

Publications

Featured Publications

KAP1 negatively regulates RNA polymerase II elongation kinetics to activate signal-induced transcription

Hyder U, Challa A, Thornton M, Nandu T, Krauss LW, D'Orso I 2024 Nature Commun

The HIV-1 Transcriptional Program: From Initiation to Elongation Control

D'Orso I 2024 J Mol Biol

HIV-1 Proviral Genome Engineering with CRISPR-Cas9 for Mechanistic Studies

Hyder U, Shukla A, Challa A, D'Orso I 2024 Viruses

Functional Analysis of KAP1/TRIM28 Requirements for HIV-1 Transcription Activation

Randolph K, Hyder U, Challa A, Perez E, D'Orso I 2024 Viruses

Mathematical Models of HIV-1 Dynamics, Transcription, and Latency

D'Orso I, Forst C 2024 Viruses

ARF alters PAF1 complex integrity to selectively repress oncogenic transcription programs upon p53 loss

Wang J, Fendler NL, Shukla A, Wu S-Y, Challa A, Lee J, Joachimiak LA, Chiang C-M, Vos SM, D'Orso I 2024 Mol Cell

ADAP1 promotes latent HIV-1 reactivation by selectively tuning KRAS-ERK-AP-1 T cell signaling-transcriptional axis.

Ramirez NP, Lee J, Zheng Y, Li L, Dennis B, Chen D, Challa A, Planelles V, Westover KD, Alto NM, D'Orso I, 2022 Mar Nat Commun 1 13 1109

KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs.

Bacon CW, Challa A, Hyder U, Shukla A, Borkar AN, Bayo J, Liu J, Wu SY, Chiang CM, Kutateladze TG, D'Orso I, 2020 May Mol. Cell

The ARF tumor suppressor targets PPM1G/PP2C? to counteract NF-?B transcription tuning cell survival and the inflammatory response.

Hyder U, McCann JL, Wang J, Fung V, Bayo J, D'Orso I, 2020 Dec Proc Natl Acad Sci U S A

An Integrated Genomics Approach Towards Deciphering Human Genome Codes Shaping HIV-1 Proviral Transcription and Fate

Ruess H, Lee J, Guzman C, Malladi, D'Orso I 2020

HIV-1 Proviral Transcription and Latency in the New Era

Shukla A, Ramirez N, D'Orso I 2020 555 12 1-40

Transcriptional Circuit Fragility Influences HIV Proviral Fate.

Morton EL, Forst CV, Zheng Y, DePaula-Silva AB, Ramirez NP, Planelles V, D'Orso I, 2019 Apr Cell Rep 1 27 154-171.e9

CDK9: A Signaling Hub for Transcriptional Control.

Bacon CW, D'Orso I 2018 Sep Transcription

The HIV-1 Tat protein recruits a ubiquitin ligase to reorganize the 7SK snRNP for transcriptional activation.

Faust TB, Li Y, Bacon CW, Jang GM, Weiss A, Jayaraman B, Newton BW, Krogan NJ, D'Orso I, Frankel AD 2018 May Elife 7

Tandem Affinity Purification of Protein Complexes from Eukaryotic Cells.

Ma Z, Fung V, D'Orso I 2017 Jan J Vis Exp 119

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction.

Guzman C, D'Orso I 2017 Aug BMC Bioinformatics 1 18 363

Transcription Elongation Control by the 7SK snRNP Complex: Releasing the Pause.

McNamara RP, Bacon CW, D'Orso I 2016 May Cell Cycle 0

Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II.

McNamara RP, Guzman C, Reeder JE, D'Orso I 2016 Mar Genom Data 7 250-5

KAP1 Recruitment of the 7SK snRNP Complex to Promoters Enables Transcription Elongation by RNA Polymerase II.

McNamara RP, Reeder JE, McMillan EA, Bacon CW, McCann JL, D'Orso I 2016 Jan Mol. Cell 1 61 39-53

7SKiing on chromatin: move globally, act locally.

D'Orso I 2016 Apr RNA Biol 0

Functional interplay between PPM1G and the transcription elongation machinery.

Gudipaty SA, D'Orso I 2016 RNA Dis 1 3

HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells.

Reeder JE, Kwak YT, McNamara RP, Forst CV, D'Orso I 2015 Oct Elife 4

PPM1G binds 7SK RNA and Hexim1 to block P-TEFb assembly into the 7SK snRNP and sustain transcription elongation.

Gudipaty SA, McNamara RP, Morton EL, D'Orso I 2015 Aug Mol. Cell. Biol.

Transcription factors mediate the enzymatic disassembly of promoter-bound 7SK snRNP to locally recruit P-TEFb for transcription elongation.

McNamara RP, McCann JL, Gudipaty SA, D'Orso I 2013 Dec Cell Rep 5 5 1256-68

Transcription control by long non-coding RNAs.

Faust T, Frankel A, D'Orso I 2012 Mar 2 3

Transition Step during Assembly of HIV Tat:P-TEFb Transcription Complexes and Transfer to TAR RNA.

D'Orso I, Jang GM, Pastuszak AW, Faust TB, Quezada E, Booth DS, Frankel AD 2012 Dec Mol. Cell. Biol. 23 32 4780-93

RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation.

D'Orso I, Frankel AD 2010 Jul Nat. Struct. Mol. Biol. 7 17 815-21

Mechanisms of eukaryotic transcription: A meeting report: August 27-31, 2013, CSHL, Cold Spring Harbor, NY.

D'Orso I 2013 Nov Transcription 5 4

Global landscape of HIV-human protein complexes.

Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ 2012 Jan Nature 7381 481 365-70

Purification and characterization of HIV-human protein complexes.

Jäger S, Gulbahce N, Cimermancic P, Kane J, He N, Chou S, D'Orso I, Fernandes J, Jang G, Frankel AD, Alber T, Zhou Q, Krogan NJ 2011 Jan Methods 1 53 13-9

HIV-1 Tat: Its Dependence on Host Factors is Crystal Clear.

D'Orso I, Frankel AD 2010 Oct 10 2 2226-2234

Host cell factors in HIV replication: meta-analysis of genome-wide studies.

Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK 2009 May PLoS Pathog. 5 5 e1000437

Tat acetylation modulates assembly of a viral-host RNA-protein transcription complex.

D'Orso I, Frankel AD 2009 Mar Proc. Natl. Acad. Sci. U.S.A. 9 106 3101-6

A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA.

Daugherty MD, D'Orso I, Frankel AD 2008 Sep Mol. Cell 6 31 824-34

Targeting tat inhibitors in the assembly of human immunodeficiency virus type 1 transcription complexes.

D'Orso I, Grunwell JR, Nakamura RL, Das C, Frankel AD 2008 Oct J. Virol. 19 82 9492-504