Alternative cleavage and polyadenylation in health and disease

Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive …

Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms

Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate …


TECtool (Terminal Exon Characterization tool) is a machine learning-based annotation software (implemented in Python) that makes use of RNA sequencing (RNA-seq) data to identify novel terminal exons, infer novel transcript isoforms and annotate potential coding sequences.

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC

3' Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(A) site use from RNA sequencing data and …


The KAPAC tool enables the identification of sequence motifs that can explain changes in cellular 3' end processing from high-throughput sequencing data.


PAQR, standing for polyadenylation site usage quantification from RNA sequencing data, allows to quantify 3' end usage from standard RNA sequencing libraries.

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogenous ribonucleoprotein C on cleavage and polyadenylation

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3’ untranslated region (3’ UTR) isoforms interact with different …


A comprehensive repository for 3' end processing sites based on a uniform analysis of a large number of 3' end sequencing data sets.

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways

The findings that microRNAs (miRNAs) are essential for early development in many species and that embryonic miRNAs can reprogram somatic cells into induced pluripotent stem cells suggest that these miRNAs act directly on transcriptional and chromatin …

Modulation of epigenetic regulators and cell fate decisions by miRNAs

Mammalian gene expression is controlled at multiple levels by a variety of regulators, including chromatin modifiers, transcription factors and miRNAs. The latter are small, ncRNAs that inhibit the expression of target mRNAs by reducing both their …