Alessandro Gardini, Ph.D.

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Wistar Institute Assistant Professor of Biochemistry and Biophysics
Department: Biochemistry and Biophysics

Contact information
The Wistar Institute
3601 Spruce Street
Philadelphia, PA 19104-4265
B.S., M.S. (Biotechnology)
University of Bologna Medical School, Italy, 2001.
Ph.D. (Molecular Medicine)
University of Milan, Italy, 2008.
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Description of Research Expertise

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In higher eukaryotes, the process of cell fate determination is at the very core of biological complexity. Genetically identical precursor cells (i.e. stem cells) can execute different transcriptional programs resulting in a wide range of differentiated cell types that are morphologically and functionally distinct. The Gardini lab works to characterize the transcriptional mechanisms that control fate choice and differentiation of human hematopoietic stem cells. In particular, we investigate how genomic regulatory sequences, termed enhancers, work to determine cell identity and specify blood lineages, such as monocytes/macrophages and granulocytes, from hematopoietic stem cells.
Furthermore, we strive to understand how large nuclear multi-protein complexes, such as Integrator and SWI/SNF, fine-tune transcription by coordinating activation of enhancers and their target promoters.

Enhancers are distal regulatory elements scattered throughout the entire genome. They play a fundamental role in orchestrating gene regulation during critical developmental processes such as cell differentiation. Furthermore, enhancers are active spots for transcription of long noncoding RNAs termed eRNAs (Gardini and Shiekhattar, 2015). These short-lived, non-polyadenylated transcripts are required to establish a link between the promoter and the distant regulatory enhancer (chromosomal looping) and contribute to the expression of the target protein-coding gene. The underlying mechanisms are poorly understood and the potential contribution of enhancers and eRNAs to cancer just started to emerge.
The lab is keen to understand how a network of enhancers drive the physiological process of hematopoiesis, and how this network is disrupted during leukemogenesis. We recently uncovered a novel enhancer regulatory axis in monocytic and macrophagic differentiation (Barbieri et al., 2018).

Integrator is a large, evolutionarily conserved, multiprotein complex that regulates several transcriptional processes. For instance, Integrator controls pause-release of RNA Polymerase II at several promoters (Gardini et. al., 2014). In addition, Integrator regulates enhancer function through the processing of noncoding eRNAs (Lai, Gardini et al., 2015). We employ a variety of genome-wide techniques, including ChIP-seq, RNA-seq, ATAC-seq and Global Run-On Sequencing (GRO-seq), along with large-scale affinity purification, to study the function of the Integrator complex in cell differentiation.

Chromatin remodelers regulate DNA accessibility by positioning nucleosomes at active promoters and enhancers. We investigate the function of SWI/SNF, the most mutated chromatin remodeler across all human cancers. Subunits of SWI/SNF, such as ARID1A, are found mutated in sporadic ovarian tumors and their specific contribution to SWI/SNF activity is poorly understood. We recently elucidated a novel function of ARID1A in pausing of RNA Polymerase II (Trizzino et al., 2018).

Transcriptional activation mediated by enhancers

Transcriptional activation mediated by enhancers.

A typical enhancer is located distal to its target protein coding locus (I) and depends on p300/CBP to maintain an open chromatin status. Binding of a sequence specific TF (II) recruits the Mediator complex (Med) to the enhancer and engages the RNAPII machinery (III) to initiate transcription on both strands. eRNAs are processed by Integrator (Int) to a mature form and bind to Mediator and Cohesin to help enforce a DNA looping between the enhancer and the distal gene (IV), culminating in activation of the target protein coding gene. (adapted from Gardini et al. FEBS J. 2015)

Selected Publications

Offley SR, Pfleiderer MM, Zucco A, Fraudeau A, Welsh SA, Razew M, Galej WP, Gardini A.: A combinatorial approach to uncover an additional Integrator subunit. Cell Rep 42: 112244, Mar 2023.

Welsh SA, Gardini A.: Genomic regulation of transcription and RNA processing by the multitasking Integrator complex. Nat Rev Mol Cell Biol 2023.

Vervoort SJ, Welsh SA, Devlin JR, Barbieri E, Knight DA, Offley S, Bjelosevic S, Costacurta M, Todorovski I, Kearney CJ, Sandow JJ, Fan Z, Blyth B, McLeod V, Vissers JHA, Pavic K, Martin BP, Gregory G, Demosthenous E, Zethoven M, Kong IY, Hawkins ED, Hogg SJ, Kelly MJ, Newbold A, Simpson KJ, Kauko O, Harvey KF, Ohlmeyer M, Westermarck J, Gray N, Gardini A, Johnstone RW.: The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer. Cell 184: 3143-3162, Jun 2021.

Trizzino M, Zucco A, Deliard S, Wang F, Barbieri E, Veglia F, Gabrilovich D, Gardini A.: EGR1 is a gatekeeper of inflammatory enhancers in human macrophages. Sci Adv 7: eaaz8836, Jan 2021.

Barbieri E, Hill C, Quesnel-Vallières M, Zucco AJ, Barash Y, Gardini A.: Rapid and Scalable Profiling of Nascent RNA with fastGRO. Cell Rep 33: 108373, Nov 2020.

Barbieri, E., Trizzino, M., Welsh, S., Owens, T., Calabretta, B., Carroll, M., Sarma, K., Gardini, A.: Targeted enhancer activation by a subunit of the Integrator complex. Molecular Cell 2018 Notes: in press.

Gardini A., Baillat D., Cesaroni M., Deqing H., Marinis JM., Wagner EJ., Lazar MA, Shilatifard A. and Shiekhattar R. : Integrator Regulates Transcriptional Initiation and Pause Release Following Activation Mol Cell 56: 128-39, 2014.

Trizzino, M., Barbieri, E., Welsh, S., Wei, S., Owens, T., Licciulli, S., Zhang, R., Gardini, A.: The tumor suppressor ARID1A controls global transcription via pausing of RNA Polymerase II. Cell Reports 2018 Notes: in press.

Gardini A.: Global Run-On Sequencing (GRO-Seq). Methods Mol Biol 2017.

Lai F. *, Gardini A.*, Zhang A. and Shiekhattar R: Integrator mediates the biogenesis of enhancer RNAs 2015 Sep 17, 525: 399-403. Nature 525: 399-403, 2015 Notes: (*equal contribution).

Chen F., Woodfin A.R., Gardini A., Rickels R.A., Marshall S.A., Smith E.R., Shiekhattar R. and Shilatifard A. : PAF1, a molecular regulator of promoter-proximal pausing by RNA Polymerase II Cell 143: 46-58, 2015.

Gardini A. and Shiekhattar R. : The many faces of long noncoding RNAs. FEBS Journal 282: 1647-1657, 2015.

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Last updated: 05/18/2023
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