Papers by Monica Ballarino
bioRxiv (Cold Spring Harbor Laboratory), Mar 19, 2024
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease for which a comprehensive know... more Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease for which a comprehensive knowledge about the pathological mechanisms is still lacking. A multitude of dysregulated cellular processes and pathways have been linked to ALS so far, including the recent focus directed toward the implication of several classes of non-coding (nc)RNAs. Within this context, the class of long ncRNAs (lncRNAs), may provide an important contribution to the onset and the severity of ALS pathogenesis, due to their high tissue specificity and their function as gene expression regulators. Nevertheless, their identification in humans often relies on differential expression analyses from bulk RNA-seq, which limits their targeting in the cellular contexts where they may be primarily involved. Here we apply dedicated pipelines to single-nucleus nuclei datasets to study lncRNA from non-pathological and prefrontal ALS human cortex. We found that in brain, distinct cell subtypes express very different pattern of lncRNAs to suggest possible roles in cellular processes found dysregulated in ALS patients. Moreover, we show the lncRNA involvement in important gene regulatory networks that result differentially regulated in pathological conditions and dissect the genomic organization of differentially expressed lncRNAs.
Stem cell investigation, Sep 19, 2016
Frontiers in Molecular Biosciences, Mar 6, 2018
The completion of the human genome sequence together with advances in sequencing technologies hav... more The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as "junk" DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.
The EMBO Journal, May 27, 2004
Stem Cells International, 2016
Pluripotent stem cells (PSCs) represent a unique kind of stem cell, as they are able to indefinit... more Pluripotent stem cells (PSCs) represent a unique kind of stem cell, as they are able to indefinitely self-renew and hold the potential to differentiate into any derivative of the three germ layers. As such, human Embryonic Stem Cells (hESCs) and human induced Pluripotent Stem Cells (hiPSCs) provide a unique opportunity for studying the earliest steps of human embryogenesis and, at the same time, are of great therapeutic interest. The molecular mechanisms underlying pluripotency represent a major field of research. Recent evidence suggests that a complex network of transcription factors, chromatin regulators, and noncoding RNAs exist in pluripotent cells to regulate the balance between self-renewal and multilineage differentiation. Regulatory noncoding RNAs come in two flavors: short and long. The first class includes microRNAs (miRNAs), which are involved in the posttranscriptional regulation of cell cycle and differentiation in PSCs. Instead, long noncoding RNAs (lncRNAs) represent a heterogeneous group of long transcripts that regulate gene expression at transcriptional and posttranscriptional levels. In this review, we focus on the role played by lncRNAs in the maintenance of pluripotency, emphasizing the interplay between lncRNAs and other pivotal regulators in PSCs.
Frontiers in Molecular Biosciences, Oct 19, 2022
Gene, Jul 1, 2004
betaTrCP mediates the ubiquitination and subsequent degradation of several key molecules thereby ... more betaTrCP mediates the ubiquitination and subsequent degradation of several key molecules thereby playing a relevant role in different cellular processes during development and in the adult. In Xenopus embryo, betaTrCP acts as a negative regulator of Wnt signaling by interacting with beta-catenin. In this paper, we report results of the study on expression and regulation of the Xenopus betaTrCP gene. We found that xbetaTrCP is expressed in Xenopus oocytes as three transcripts, which very likely correspond to the previously identified localized mRNAs, and four isoforms. The xbetaTrCP promoter functional and structural analysis showed the presence of elements target of positive transcriptional control. Among them, we have identified a beta-catenin/Tcf signaling responsive region and a 45-bp element containing a sequence motif conforming to the SRF binding site, closer to the transcription initiation sites. There are also elements of transcriptional negative control.
Biochimica et biophysica acta (N), Aug 1, 2002
hTrCP plays a relevant role in the control of stability of several key protein factors. In Xenopu... more hTrCP plays a relevant role in the control of stability of several key protein factors. In Xenopus, hTrCP acts as an inhibitor of Wnt signaling and dorsal axis formation. We determined the primary structure of the frog hTrCP gene, which consists of 14 exons and 13 introns, spanning over 34 kb. Isoforms of x-hTrCP have been found, which show differences in the NH 2 and COOH regions. NH 2 isoforms differ for the presence or absence of a 30 aa sequence, coded by exon III. In COOH isoforms, 19 C-terminal amino acids are replaced by three different amino acids. Occurrence of two 5V splice donor sites for splicing of intron XIII provides an explanation for these isoforms, based on alternative splicing. The DNA region of the putative hTrCP promoter contains several TATA elements, one GCCAAT box, and putative binding sites for Ets, Tcf/Lef and NF-nB transcription factors. Two transcription initiation sites have been mapped downstream of TATA boxes proximal to ATG for start of translation. Comparison of the Xenopus and human hTrCP genes indicates high conservation of exon nucleotide and amino acid sequences, size and organization; differences are limited to exons coding for N-and C-terminal regions.
eLife, Jan 12, 2021
Skeletal muscle possesses an outstanding capacity to regenerate upon injury due to the adult musc... more Skeletal muscle possesses an outstanding capacity to regenerate upon injury due to the adult muscle stem cell (MuSC) activity. This ability requires the proper balance between MuSC expansion and differentiation, which is critical for muscle homeostasis and contributes, if deregulated, to muscle diseases. Here, we functionally characterize a novel chromatin-associated long noncoding RNA (lncRNA), Lnc-Rewind, which is expressed in murine MuSCs and conserved in human. We find that, in mouse, Lnc-Rewind acts as an epigenetic regulator of MuSC proliferation and expansion by influencing the expression of skeletal muscle genes and several components of the WNT (Wingless-INT) signalling pathway. Among them, we identified the nearby Wnt7b gene as a direct Lnc-Rewind target. We show that Lnc-Rewind interacts with the G9a histone lysine methyltransferase and mediates the in cis repression of Wnt7b by H3K9me2 deposition. Overall, these findings provide novel insights into the epigenetic regulation of adult muscle stem cells fate by lncRNAs.
Journal of Clinical Investigation, Jun 1, 2016
ChemMedChem, Feb 2, 2014
CHEMMEDCHEM MINIREVIEWS Ricerca" (FIRB) and "Research Projects of National Interest" (PRIN).
Molecular and Cellular Biology, Jul 1, 2005
The carboxy-terminal domain (CTD) of RNA polymerase II large subunit acts as a platform to assemb... more The carboxy-terminal domain (CTD) of RNA polymerase II large subunit acts as a platform to assemble the RNA processing machinery in a controlled way throughout the transcription cycle. In yeast, recent findings revealed a physical connection between phospho-CTD, generated by the Ctk1p kinase, and protein factors having a function in small nucleolar RNA (snoRNA) biogenesis. The snoRNAs represent a large family of polymerase II noncoding transcripts that are associated with highly conserved polypeptides to form stable ribonucleoprotein particles (snoRNPs). In this work, we have studied the biogenesis of the snoRNPs belonging to the box H/ACA class. We report that the assembly factor Naf1p and the core components Cbf5p and Nhp2p are recruited on H/ACA snoRNA genes very early during transcription. We also show that the cotranscriptional recruitment of Naf1p and Cbf5p is Ctk1p dependent and that Ctk1p and Cbf5p are required for preventing the readthrough into the snoRNA downstream genes. All these data suggest that proper cotranscriptional snoRNP assembly controls 3-end formation of snoRNAs and, consequently, the release of a functional particle.
Nature Structural & Molecular Biology, Aug 31, 2008
microRNAs (miRNAs) are generated from long primary (pri-) RNA polymerase II (Pol II)-derived tran... more microRNAs (miRNAs) are generated from long primary (pri-) RNA polymerase II (Pol II)-derived transcripts by two RNase III processing reactions: Drosha cleavage of nuclear pri-miRNAs and Dicer cleavage of cytoplasmic pre-miRNAs. Here we show that Drosha cleavage occurs during transcription acting on both independently transcribed and intron-encoded miRNAs. We also show that both 5′-3′ and 3′-5′ exonucleases associate with the sites where co-transcriptional Drosha cleavage occurs, promoting intron degradation before splicing. We finally demonstrate that miRNAs can also derive from 3′ flanking transcripts of Pol II genes. Our results demonstrate that multiple miRNA-containing transcripts are co-transcriptionally cleaved during their synthesis and suggest that exonucleolytic degradation from Drosha cleavage sites in pre-mRNAs may influence the splicing and maturation of numerous mRNAs. miRNAs belong to a growing class of conserved noncoding transcripts, 21-23 nucleotides (nt) long, that regulate the fine tuning of gene expression by RNA-mediated gene-silencing mechanisms 1. They derive from a longer primary transcript, the pri-miRNA, by a stepwise process that occurs in both nuclear and cytoplasmic compartments. In the nucleus, the Microprocessor complex containing Drosha, an RNase III like enzyme, and its cofactor DGCR8 generates a pre-miRNA hairpin product about 70 nt long 2-4. Pri-miRNA processing represents a crucial step in miRNA biogenesis because it defines the miRNA sequences embedded in long pri-miRNAs and generates one end of the mature miRNA molecule. DGCR8 is thought to recognize the junction between the single-and double-stranded region (SD junction) and the 33-base pair (bp) stem of the pri-miRNA substrate. The doublestranded RNA (dsRNA) binding domain (dsRBD) of Drosha may then transiently interact Correspondence should be addressed to N.J.P.
Molecular and Cellular Biology, Jun 15, 2018
Page 730, Fig. 1B: During assembly, the PCR amplification for lnc-803 was an erroneous duplicatio... more Page 730, Fig. 1B: During assembly, the PCR amplification for lnc-803 was an erroneous duplication of the lnc-776 panel. The correct lnc-803 panel is shown below. This mistake does not change the results, since both lncRNAs similarly increase during differentiation. Page 730, Fig. 1C: The lnc-686 panel was accidentally flipped; the corrected orientation is shown below. We are very sorry for these oversights.
Current stem cell research & therapy, Nov 10, 2020
Large scale projects such as FANTOM and ENCODE led to a revolution in our comprehension of the ma... more Large scale projects such as FANTOM and ENCODE led to a revolution in our comprehension of the mammalian transcriptomes by revealing that ~53% of the produced RNAs do not encode for proteins. These transcripts, defined as noncoding RNAs (ncRNAs), constitute a heterogeneous group of molecules which can be categorized in two main classes, namely small and long, according to their length. In animals, the first-class includes Piwi-interacting RNAs (piRNAs), small interfering RNAs (siRNAs) and microRNAs (miRNAs). Among them, the best-characterized subgroup is represented by miRNAs, which are known to regulate gene expression largely at the post-transcriptional level. In contrast, long noncoding RNAs (lncRNAs) represent a more heterogeneous group of > 200 nucleotides long transcripts, that act through a variety of mechanisms at both transcriptional and posttranscriptional level. Here, we discuss how miRNAs and lncRNAs are emerging as pivotal regulators of cardiac muscle development and how the alteration of ncRNA expression was seen to disturb the physiology of all the different cell types forming the cardiac tissue. Particular emphasis is given to those species that are expressed and are known to regulate the capacity of cardiac progenitor cells (CPCs), currently used in regenerative medicine protocols, to proliferate and differentiate. Understanding how the ncRNAmediated circuitries regulate heart homeostasis is one of the research areas expected to have a high impact, improving the therapeutic efficacy of stem/progenitor-cells treatments for translation into clinical applications.
Cold Spring Harbor Symposia on Quantitative Biology, 2006
Oncogene, Nov 5, 2012
TAF15 (formerly TAFII68) is a member of the FET (FUS, EWS, TAF15) family of RNA-and DNA-binding p... more TAF15 (formerly TAFII68) is a member of the FET (FUS, EWS, TAF15) family of RNA-and DNA-binding proteins whose genes are frequently translocated in sarcomas. By performing global gene expression profiling, we found that TAF15 knockdown affects the expression of a large subset of genes, of which a significant percentage is involved in cell cycle and cell death. In agreement, TAF15 depletion had a growth-inhibitory effect and resulted in increased apoptosis. Among the TAF15-regulated genes, targets of microRNAs (miRNAs) generated from the onco-miR-17 locus were overrepresented, with CDKN1A/p21 being the top miRNAstargeted gene. Interestingly, the levels of onco-miR-17 locus coded miRNAs (miR-17-5p and miR-20a) were decreased upon TAF15 depletion and shown to affect the post-transcriptional regulation of TAF15-dependent genes, such as CDKN1A/p21. Thus, our results demonstrate that TAF15 is required to regulate gene expression of cell cycle regulatory genes post-transcriptionally through a pathway involving miRNAs. The findings that high TAF15 levels are needed for rapid cellular proliferation and that endogenous TAF15 levels decrease during differentiation strongly suggest that TAF15 is a key regulator of maintaining a highly proliferative rate of cellular homeostasis.
Molecular Neurobiology, Oct 11, 2013
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Papers by Monica Ballarino