Research Projects

RNA Editing

A-to-I RNA editing is a post-transcriptional mechanism in which gnomically encoded

Adenosine (A) is converted to Inosine (I) in the corresponding RNA, transcribed from

the same locus.

This type of editing is catalyzed by ADAR enzymes, which target double-stranded RNA

substrates.

The Inosine in the edited RNA is recognized by the cellular machineries as Guanosine (G).

This changes the genomic code and increases the diversity of the transcriptome.

The complexity of the molecular machinery that mediates A-to-I editing and the number

of editing targets seems to increase from lower to higher organisms.

Moreover, ADAR mediated RNA editing has proven to be important for normal brain function, and diseases of the central nervous system, such as depression, epilepsy, schizophrenia and ALS have been linked to a deregulation of RNA editing.

In recent years, bioinformatics approaches were used to find editing sites and to estimate the prevalence of RNA editing in the human genome. Mismatch results of RNA transcripts alignment with the genome are considered editing candidates. The outcome of these approaches has revealed a few thousand new editing sites. Most of them were found in Alu repeats.

Alu repeats are very common in the human genome with more than million copies, and are characterized by low divergence. Thus, many genes may contain two similar and reversely oriented elements which are likely to form a double-stranded RNA structure, which is the preferred target for RNA editing. We assume that RNA editing is a much more common phenomenon, occurring in the human genome more frequently than has been shown up till now.

The upcoming high-throughput sequencing methods offer an increased coverage and depth of the sequenced transcriptome, which will allow us a better identification of the edited sites and characterization of the RNA editing phenomenon.

 

 

Somatic Activity of Retrotransposons in Human

R. Cordaux and M. A. Batzer. "The impact of retrotransposons on human

genome evolution". Nat. Rev. Genet. 10, 691-703 (2009).

Retrotransposons’ activity can cause dramatic changes in the human’s genome.

Therefore, exploring their activity and its influence arouses great interest.

Retrotransposons are genomic sequences that duplicate in a “copy-paste”

mechanism through an RNA intermediate followed by reverse transcription

and insertion into a new genomic location.

Insertion events in protein-coding or regulatory regions can alter genome

function, contribute to genetic innovation and impacts the evolution of primate

genomes in terms of both structure and function. 

L1, Alu and SVA retrotransposons, who collectively account for approximately

one-third of the human genome, are the only transposable elements currently

known to be active in humans. The large-scale studies of retrotransposon are

now possible due to huge development in next generation sequencing.

This research area is relatively new and of great interest, due to the fact that

retrotransposons continue to produce genetic diversity in humans, and also

cause diseases as a result of their integration into genes. In this research, we study the somatic activity of retrotransposons in the human genome using next generation sequencing data. We focus mainly on characterizing retrotransposons in the human genome, identifying recent events of insertion and comparing the expression levels of retrotransposons in various tissues.

Research description : Identification of DNA editing sites. APOBEC3 mammalian proteins are able to induce C-to-U mutations in retrotransposons during reverse transcription. This led to numerous apparent G-to-A mutations between extant retrotransposon copies that might have dramatically affected their evolution. We are working on computational identification and characterization of those sites in various genomes and are examining intra- and inter-genomic diversity of DNA editing rates and patterns.

 

DNA editing of mammalian genomes


The ability of retrotransposons to spread DNA fragments throughout the

genome had an extremely important role in evolution and led to formation

of new exons, genes, and gene regulation networks. However, the processes

shaping the evolution and adaptation of retrotransposons are still unclear.


We showed that DNA editing, an antiviral mechanism, accelerated the

evolution of mammalian genomes by large-scale modification of their

retrotransposon. The modification is apparent as numerous extant

retrotransposons bearing long clusters of G-to-A mutations, which are the

hallmark of APOBEC3 activity, an antiviral protein. Since DNA editing

generates a large number of mutations simultaneously, each affected element

begins its evolutionary trajectory from a unique starting point, thereby

increasing the probability of developing a novel function.


Our current research is focused on developing advanced statistical methods for systematic DNA editing detection, characterization of editing sites in human and other genomes and their role in evolution, and studying the effect of DNA editing on human variation. Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G, Furukawa et al., The EMBO Journal 28, 440 (2009).

 

Alternative Splicing

A single human gene expresses a pre-mRNA which contains an average of eight

exons separated by long non-coding introns. Alternative pathways of intron removal

(alternative splicing) are now assumed to occur in the vast majority of human

pre-mRNAs. After realization that there are fewer human genes than originally

anticipated, alternative splicing is now considered the leading driver for human

protein diversity.

However, although alternative splicing has been a well-studied process for the last

30 years, its complex regulation and consequences are still mostly decrypted.

High-throughput sequencing technologies give an opportunity to address the

open questions in the field. Using targeted RNA sequencing (padlock technology)

we are able to zoom-in and profile differences in alternative splicing between different tissues.

A better understanding of this fundamental process is bound to provide substantial gains in comprehension of other cellular processes.

Moreover, many human diseases, such as cancer and Alzheimer disease, are closely linked to alternative splicing.