Biology subjects

Ntini, E.

Publications and source records attributed to Ntini, E..

3 recordsLinked to original sources

bioRxiv2018

Transient N-6-methyladensosine Transcriptome sequencing reveals a regulatory role of m6A in splicing efficiency

Splicing efficiency varies among transcripts, and tight control of splicing kinetics is crucial for coordinated gene expression. N-6-methyladenosine (m6A) is the most abundant RNA modification and is involved in regulation of RNA biogenesis and function. The impact of m6A on the regulation of RNA splicing kinetics has not been investigated. Here, we provide the first time-resolved high-resolution assessment of m6A on nascent RNA transcripts and unveil its importance for the control of RNA splicing kinetics. We identify that early co-transcriptional m6A deposition near splice junctions promotes fast splicing, while m6A modification of introns is associated with long, slowly processed introns and alternative splicing events. In conclusion, by directly comparing the processing dynamics of individual transcripts in the methylated versus unmethylated state on a transcriptome-wide scale we show that early m6A deposition marks transcripts for a fast-track processing.

molecular biology↗

bioRxiv2017

Chromatin-release of the long ncRNA A-ROD is required for transcriptional activation of its target gene DKK1

Long non-coding RNAs (ncRNAs) are involved in both positive and negative regulation of transcription. Long ncRNAs are often enriched in the nucleus and at chromatin but whether chromatin-release plays a functional role is unknown. Here, we used epigenetic marks, expression level and strength of chromatin interactions to group long ncRNAs and find that those engaged in strong chromatin interactions are less enriched at chromatin in MCF-7 cells, suggesting a functional involvement of chromatin-release of long ncRNAs in transcriptional regulation. To study this further, we identify the long ncRNA A-ROD, an activating regulator of the Wnt signaling inhibitor DKK1. We show that A-ROD enhances transcription elongation of DKK1 in an RNA-dependent manner and that A-ROD recruits EBP1 to the DKK1 promoter. Our data suggest that the activating function depends on the release of A-ROD from chromatin, and further identify a functional regulatory interaction mediated by A-ROD in the transcription activation of DKK1. We propose that the release of a subset of long ncRNAs is important for their function, adding a new mechanistic perspective to the subcellular localization of long ncRNAs.

molecular biology↗

bioRxiv2016

Microprocessor dynamics shows co- and post-transcriptional processingof pri-miRNAs

miRNAs are small regulatory RNAs involved in the regulation of translation of target transcripts. miRNA biogenesis is a multi-step process starting with the cleavage of the primary miRNA transcript in the nucleus by the Microprocessor complex. Endogenous processing of pri-miRNAs is challenging to study and the in vivo kinetics of this process is not known. Here, we present a method for determining the processing kinetics of pri-miRNAs within intact cells over time using a pulse-chase approach to obtain nascent RNA within a 1-hour window after labeling with bromouridine. We show, that pri-miRNAs exhibit different processing kinetics ranging from fast over intermediate to slow processing and provide evidence that pri-miRNA processing can occur both co-transcriptionally and post-transcriptionally.

molecular biology↗