Epigenomics and Transcriptional Regulation

Transcript’s abundance is typically considered a proxy of the corresponding gene’s transcriptional activity. Yet, a poorly transcribed gene could see many of its RNA molecules accumulate just because they are highly stable. Conversely, if a gene is very actively transcribed but its transcripts are highly unstable, only a few copies of its RNAs are found in the cell. Indeed, RNA abundance and its variation arise from the combined action of cellular machineries responsible for the synthesis of novel transcripts, their processing into mature species, and the degradation of the latter (see Furlan M et al, Briefings in Bioinformatics 2020, for a recent review on this subject from our group).

Our lab studies the dynamics of RNA metabolism (henceforth RNA dynamics), and aims at:
  1. deciphering how RNA dynamics are shaped by epitranscriptional RNA modifications
  2. characterizing the role of RNA dynamics in gene expression programs orchestrated by transcription factors such as the MYC oncogene
  3. revealing how aberrant RNA modifications lead to altered RNA dynamics in cancer.

These objectives are pursued through a unique interdisciplinary approach that combines experimental and computational methods, including RNA metabolic labeling and epitranscriptome profiling together with their integrated analysis through mathematical modeling. This reflects into the current composition of the group, which includes an established computational part tightly collaborating with a more recent experimental part.


Outline

Contacts

Mattia Pelizzola
This email address is being protected from spambots. You need JavaScript enabled to view it.
Twitter: @MattiaPelizzola
(+39) 02 94 375 019

 

Current and ongoing research

Development of novel approaches for the study of RNA dynamics

The characterization of RNA dynamics is typically based on the joint profiling of total and nascent RNAs, the latter profiled through RNA metabolic labeling. The integrative analysis of these data, which ultimately allows disentangling pre-existing from newly synthetized transcripts, allows us to decipher how gene expression programs are established by the balance of synthesis, processing and degradation. Achievements and ongoing activity:
  • The development of INSPEcT (de Pretis S et al., Bioinformatics 2015), which allowed for the first time the comprehensive analysis of RNA dynamics.
  • We developed a novel version of INSPEcT, which allows the quantification of RNA dynamics without requiring the quantification of nascent RNA (Furlan M et al., Genome Res 2020).
  • INSPEcT was used to characterize how the activation of MYC impacts RNA dynamics (de Pretis et al., Genome Res 2017; Tesi A et al., EMBO Reports 2019). These studies provided unprecedented details on how this fundamental transcription factor and oncogene controls the transcription of thousands of target genes.

Dynamics

 

Development of novel approaches for the study of RNA Polymerase II (RNAPII) dynamics

RNAPII is a key actor in genes’ transcription and a complex regulatory hub. The life-cycle of the RNAPII complex includes its recruitment and assembly to promoters, followed by pause-release, elongation, and detachment from the 3’ end of genes. Most of the studies dealing with the RNAPII life-cycle rely on ChIP-seq data, while it has been shown that these are unable to univocally quantify the dynamics of each step. For example, a variation in the density of RNAPII bound to promoters can be due to a change in either its recruitment or in its pause-release rate (or both). We recently developed a method to properly address this issue (de Pretis et al., Genome Res 2017), which was used to provide critical insights on the mechanisms through which MYC modulates its targets. Achievements and ongoing activity:
  • The development of a computational method that allows the quantification of the kinetic rates of RNAPII recruitment, pause-release, elongation and detachment (de Pretis et al., Genome Res 2017).
  • This method, applied in the context of MYC activation, revealed that the most prominent effect of the binding of this factor is not the promotion of pause-release, as previously suggested, while RNAPII recruitment (de Pretis et al., Genome Res 2017; Tesi A. et al., EMBO Reports 2019). Moreover, this suggested that MYC primarily acts as an activator, as recently independently confirmed. These data indeed suggest that the repression of a subset of MYC target genes is mostly a passive consequence acute MYC activation.
  • We are developing a novel method, relying on RNA metabolic labeling and single molecule Nanopore sequencing, to study the impact of RNA modifications on RNA and RNAPII dynamics at the level of single isoforms.

 

The role of the m6A-epitranscriptome in cancer

Despite the rapid progress in the field, various aspects of the functional role of this mark remain poorly characterized. We are far from a complete understanding of how m6A influences the dynamics of marked transcripts, and we are just at the beginning in understanding the crosstalk between the m6A machinery and chromatin regulation. Moreover, and more importantly, we just started appreciating how the epitranscriptome could shape aberrant gene expression programs in cancer. Ongoing activity in the lab, supported through a grant and a fellowship from AIRC:
  • We are studying the role of the m6A epitranscriptome in the context of MYC-driven aberrant transcriptional programs in breast cancer.
  • We are characterizing the role of the m6A epitranscriptome in the context of drug resistance in Hepatocellular Carcinoma.

Group Members

Mattia Pelizzola - PI

Computational:

  • Mattia Furlan - theoretical physicist (postdoc): mathematical modeling of RNA dynamics
  • Francesca Ratti - engineer (PhD student @PoliMi): mathematical modeling of RNAPII dynamics
  • Roberto Albanese - bioinformatician (Master student @UniMi): (epi)transcriptional dynamics through Nanopore data

Wet-lab:

  • Lucia Coscujuela - molecular biologist (postdoc): role of the m6A epitranscriptome in liver cancer
  • Iris Tanaka - molecular biologist (postdoc): role of the m6A epitranscriptome in breast cancer
  • Nunzio del Gaudio - visiting molecular biologist (postdoc): (epi)transcriptional dynamics in cancer

News

  • We are looking for a computational postdoc, more info here! Candidates eligible to MSCA fellowship are encouraged [May 2021]
  • Good luck to Stefano de Pretis, for many years computational scientist in the group, now at HSR [Jan 2021]
  • A great start of 2021 with a grant to the lab and a fellowship to Lucia, both funded by AIRC to study m6A and RNA dynamics in cancer [Jan 2021]
  • Welcome Francesca and Roberto in the group! [Sep 2020]
  • Congratulations to Eugenia Galeota for her novel appointment at INGM [Apr 2020]
  • We are co-editing a special issue on the role of RNA modifications - Epigenomes MDPI [Feb 2020]
  • Welcome Lucia in the group! [Nov 2019]
  • Welcome Iris in the group! [Aug 2019]
  • We are co-editing a special issue on Computational Epitranscriptomics - Frontiers In Genetics [Apr 2019]
  • A postdoctoral position for a molecular biologist is open! [Jan 2019]
  • Eugenia's 2017 paper nominated in the 2018 Best Paper Selection by the International Medical Informatics Association [Sep 2018]
  • European Epitranscriptomic Network (EPITRAN): the position paper was published [May 2018]
  • One PhD position is open for a computational or experimental PhD student [May 2018]
  • Welcome Nunzio in the group! [Mar 2018]
  • Congratulations to Stefano for the Cover in the October Genome Research issue! [Oct 2017]

 

  

 Cover

Recent Publications

For the complete list please refer to our Google Scholar page.

  1. de Pretis S .. Pelizzola M (2021). Identification of Genes Post-Transcriptionally Regulated from RNA-seq: The Case Study of Liver Hepatocellular Carcinoma. Methods Mol Biol
  2. Furlan M .. Pelizzola M (2020). Dynamics of transcriptional and post-transcriptional regulation. Briefings in Bioinformatics
  3. Furlan M .. Pelizzola M (2020). Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Research
  4. de Pretis S .. Pelizzola M (2020). INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. Frontiers in Genetics
  5. Furlan M .. Pelizzola M (2020). Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts. Frontiers in Genetics
  6. Galeota E, Pelizzola M (2020). Ontology-driven integrative analysis of omics data through Onassis. Scientific Reports
  7. Furlan M .. Pelizzola M (2019). m6A-Dependent RNA Dynamics in T Cell Differentiation. Genes
  8. de Pretis S .. Pelizzola M (2017). Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation. Genome Research
  9. Galeota E, Pelizzola M (2017). Ontology-based annotations and semantic relations in large-scale (epi)genomics data. Briefings in Bioinformatics
  10. de Pretis S .. Pelizzola M (2015). INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. Bioinformatics
  11. Kishore K .. Pelizzola M (2015). methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics
  12. Sabò A*, Kress TR*, Pelizzola M*, .. , Amati B (2014). Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature

* indicates co-authorship.