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Alessandro Gardini, Ph.D.

Alessandro Gardini, Ph.D.

Laboratory

The Gardini Laboratory

Contact

215-898-3785
agardini@wistar.org

https://twitter.com/GardiniLab 

Assistant Professor, Gene Expression & Regulation Program, The Wistar Institute Cancer Center

About the Scientist

Gardini studies the epigenetic control of transcription during cell differentiation and oncogenesis.

Born and raised in Italy, Gardini obtained a B.S./M.S. in medical biotechnology at the University of Bologna and attended the graduate school of Molecular Medicine at the University of Milan. He trained as a postdoctoral fellow with Dr. Ramin Shiekhattar at the Center of Genomic Regulation in Barcelona, The Wistar Institute and the University of Miami Medical School. He joined Wistar as an assistant professor in 2015. Gardini is a scholar of the Leukemia Research Foundation and the American Cancer Society.

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The Gardini Laboratory

Transcriptional regulation is a multi-layer process carried out by specialized transcription factors, co-factors and enzymatic machineries working within the context of a structured chromatin landscape.

We use a combination of genomics, proteomics and biochemistry to investigate how basal transcriptional complexes and epigenetic modulators orchestrate gene expression in normal and tumor cells.


A.Gardini - Image 1

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Staff

Postdoctoral Fellows

Sandra Deliard, Ph.D.
Avery Zucco, Ph.D.
Yingjie Zhang, Ph.D.

Graduate Students

Connor Hill (UPenn-CAMB)
Sarah Offley (UPenn-CAMB)
Sarah Welsh (UPenn-BMB)
Martina Gatto (UniBO)

Lab Assistant

Steven Ly

ALUMNI

Marco Trizzino, Ph.D. (2016-2019), assistant professor, Thomas Jefferson University 

Elisa Barbieri, Ph.D. (2015-2019), Marie Sklodowska-Curie Fellow, University of Edinburgh

Available Positions

Motivated candidates are encouraged to inquire about the positions below. Contact agardini@wistar.org.

Postdoctoral Fellow
Graduate Students (BGS-UPenn)

Research

We dissect the transcriptional mechanisms that control fate choice and differentiation of human hematopoietic cells, particularly in the myeloid compartment. We are especially interested in the role of transcriptional enhancers

Enhancers are distal regulatory elements, scattered throughout the entire genome, that direct gene regulation during development. Furthermore, enhancers are active spots for transcription of long noncoding 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 has just started to emerge. The lab is keen on understanding how enhancer networks get activated and promote differentiation of myeloid cells, and how this process is disrupted during leukemogenesis. We recently uncovered a novel enhancer regulatory axis in myeloid progenitor cells (Barbieri, Trizzino et al., 2018), centered around the EGR-1 transcription factor and a newly characterized module of the Integrator complex. 


Enhancer priming and activation by the INTS13-EGR1 axis (Barbieri, Trizzino et al., 2018) - FINAL Image

 

Additional studies (Trizzino, Zucco et al., in press) revealed that EGR-1 also coordinates a repressive activity, independent of Integrator, in mature macrophages. Particularly, EGR-1 restrains the activity of inflammatory enhancers and effectively curbs the response of macrophages to inflammatory stimuli.

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Eukaryotic transcription pivots around the balanced activity of kinases and phosphatases that regulate the transcription initiation, early elongation and termination checkpoints. While the dynamic recruitment of kinases (i.e. CDK7, CDK9) and their cognate cyclins have been studied for many years, the association of phosphatases with active transcription has been largely understudied. We recently uncovered that protein phosphatase 2A (PP2A) is recruited at the pause-release checkpoint where it opposes CDK9 activity (Vervoort, Welsh et al., 2020). We found that the Integrator subunit INTS6 draws PP2A to the transcription bubble to dephosphorylate the RNAPII-CTD (especially Ser2) and maintain polymerase in a paused conformation. PP2A activity is frequently lost in cancer and restoring its ability to curb transcription opens up new therapeutic strategies for tumors ‘addicted’ to transcriptional elongation.


Regulation of transcription by the PP2A phosphatase (A. Gardini – created with BioRender) - Image 2

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Integrator is a large, evolutionarily conserved, multiprotein complex that is quickly emerging as a centerpiece of transcriptional regulation in higher eukaryotes. The Integrator complex is a regulatory hub for several transcriptional and epigenetic processes. For instance, Integrator’s INTS11 subunit controls release of RNA Polymerase II at promoters via endonucleolytic cut of nascent RNA (Gardini et al., 2014; Beckedorff et al., 2020). In addition, INTS11 regulates enhancer function through the processing of noncoding eRNAs (Lai, Gardini et al., 2015). We identified a new functional module of Integrator, centered around the INTS13 subunit, that prompts enhancer activation in myeloid cells (Barbieri, Trizzino et al., 2018). More recently, we showed that the INTS6/INTS8 subunits of the complex recruit the PP2A phosphatase to chromatin, to control phosphorylation of the RNAPII-CTD as well as other polymerase co-factors implicated in pausing and elongation (Vervoort, Welsh et al., 2020). Notably, Integrator subunits are found mutated in developmental diseases and are frequently lost in certain tumor types. The lab keeps pursuing the biochemical and functional dissection of all 14 subunits of the Integrator complex. 


Multifaceted role of Integrator in transcription and epigenetic regulation

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Conventional transcriptomic analyses (i.e. ribo-depleted RNA-seq, 3’-seq) offer a glimpse into global gene regulation but often fail to convey the most accurate picture. Because RNA-seq captures steady-state and cytoplasmic transcripts, changes in gene expression can be hindered by RNA stability. Furthermore, RNA Polymerase dynamics is only revealed by real-time nascent RNA transcription. We strive to implement and optimize techniques of nascent RNA-seq, improving their reproducibility and applicability. To this purpose, we recently developed fastGRO (Barbieri, Hill et al., 2020) as a global nuclear run-on assay of rapid execution and suitable for primary cells.    


Profiling Human Transcriptomes at Better Resolution - Image 4

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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).
  

Selected Publications

Barbieri, E., Hill, C., Quesnel-Vallières, M., Zucco, A.J., Barash, Y., Gardini, A. "Rapid and Scalable Profiling of Nascent RNA with fastGRO" Cell Rep. 2020 Nov 10;33(6):108373. doi:10.1016/j.celrep.2020.108373.

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

Trizzino, M., Barbieri, E., Petracovici, A., Wu, S., Welsh, S.A., Owens, T.A., Licciulli, S., Zhang, R., Gardini, A. "The tumor suppressor ARID1A controls global transcription via pausing of RNA Polymerase II." Cell Reports. 2018.

Lai, F., Gardini, A., Zhang, A., Shiekhattar, R. "Integrator mediates the biogenesis of enhancer RNAs." Nature. 2015 Sep 17;525(7569):399-403. doi: 10.1038/nature14906. Epub 2015 Aug 26.

Gardini, A., Shiekhattar, R. "The many faces of long noncoding RNAs." FEBS J. 2015 May;282(9):1647-57. doi: 10.1111/febs.13101. Epub 2014 Nov 7.

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