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Competitive endogenous (ce)RNAs cross-regulate each other through sequestration of shared microRNAs and form complex regulatory networks based on their microRNA signature. However, the molecular requirements for ceRNA cross-regulation and the extent of ceRNA networks remain unknown. Here, we present a mathematical mass-action model to determine the optimal(More)
MicroRNAs are endogenous non-coding RNAs which negatively regulate the expression of protein-coding genes in plants and animals. They are known to play an important role in several biological processes and, together with transcription factors, form a complex and highly interconnected regulatory network. Looking at the structure of this network, it is(More)
MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to tissue morphogenesis, and their aberrant behavior is often associated with the development of various diseases. Recently it(More)
BACKGROUND The MYC transcription factors are known to be involved in the biology of many human cancer types. But little is known about the Myc/microRNAs cooperation in the regulation of genes at the transcriptional and post-transcriptional level. METHODOLOGY/PRINCIPAL FINDINGS Employing independent databases with experimentally validated data, we(More)
It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a Transcription Factor (TF) which regulates the other targets. This combination defines a new class of feed-forward loops (FFLs) in(More)
MicroRNAs, post-transcriptional repressors of gene expression, play a pivotal role in gene regulatory networks. They are involved in core cellular processes and their dysregulation is associated to a broad range of human diseases. This paper focus on a minimal microRNA-mediated regulatory circuit, in which a protein-coding gene (host gene) is targeted by a(More)
Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other’s expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are(More)
A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes " Submitted " CircuitsDB_2: integrating long non-coding RNAs into the cancer genes regulatory network " In preparation The Road goes ever on and on Down from the door where it began. Now far ahead the Road has gone, And I must(More)
gene expression Marco Del Giudice, 2, ∗ Stefano Bo, Silvia Grigolon, † and Carla Bosia ∗,†,1, 2 1Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy 2Human Genetics Foundation, via Nizza 52, I-10126 Torino, Italy 3Nordita, Royal Institute of Technology and Stockholm University,(More)