Noncoding RNAs in Development and Cancer 2013

Keystone Symposia

Highlights

The meeting’s focus was equally divided between miRNAs and other non-coding RNAs , which was also reflected in the opening Keynote Session that included both a speech on long non-coding RNAs from Dr. Jeannie Lee and a speech on miRNAs from Dr. Narry Kim.

Connection of miRNAs with oncogenic mechanisms dominated most of the poster sessions as well as many speaker sessions but the meeting also included a substantial amount of novel data on mechanisms governing long non-coding RNA impact on chromatin as well as stem cell differentiation.

Interestingly, a whole session was devoted to possible therapeutic applications of non-coding RNAs with some of the largest companies in the filed unfolding their current strategies. Although this session focused on miRNAs, the therapeutic potential  of other non-coding RNAs was also “touched” both in the keynote as well as the poster session.

Moreover, throughout the sessions of this meeting there was an evident attempt to move from just describing the connection of non-coding RNAs with basic developmental and cellular processes towards a more mechanistic insight into the exact proteins and chromatin modifiers/modifications underlying these effects.

To this end, the meeting and especially the poster sessions included, not only a substantial number of genome wide ChIP and RNA-seq data, but also RNA structural and extended functional assays involving key chromatin players. Finally, in many instances (especially posters) the meeting extended also beyond cancer and development to include a more wide disease spectrum such as cardiovascular and reproduction.

 Long Non-Coding RNAs and Epigenetic Regulation

Dr. Jeannie Lee Harvard Medical School

The first part of this keynote session included some exciting new data on an unexpected connection of Xist with hematopoietic development and a connection with the respective malignancies when conditionally deleted.  Given the fact that Xist until now had been connected mainly with  X chromosome inactivation, the speaker denoted the hidden functional  potential of Xist in cases other than X inactivation, especially regarding epigenetic regulation and the resulting dose compensation effects.

This interplay of non-coding RNAs with  the epigenome was further elaborated by the speaker in the case of PRC2 presenting her previous work on RNAs that were found to be bound by Ezh2 via RIP-seq as well as the way that Ezh2 signals and the respective H3k27me3 are spreading during X inactivation.

A very interesting part of this talk was when she presented a model in which this spreading takes place via specific “chromatin”stations across the mouse genome in which these signals are stronger. Since, as she noted, PRC2 regulation is a general phenomenon , X inactivation could serve as a good example on how this kind of regulation through ncRNAs takes place and reveal a new therapeutic potential for these RNAs. This potential was the last part of her talk in which she presented ways  that targeting RNAs could regulate protein coding gene expression.

Biogenesis and Regulation of MicroRNA

Dr. Narry Kim, Seoul National University

In this second keynote lecture, Dr Kim presented recent findings on post-transcriptional control of miRNA function.  After a small introduction in her previous work on miRNA biogenesis she elaborated on the question how 3’end  modifications work to control miRNA processing. She presented a combination of RNA-seq and CLIP-seq  (for Lin28A)  data  and showed that  oligo- and mono- uridylation play a key role in miRNA processing and stability at least in case of members of let-7 family.

Particularly, Lin28 binds to miRNA precursor  serving as cofactor for nucleotidyl transferases . Dr Kim revealed a Lin-28 binding motif inferred from CLIP-seq data, which is present in a 5-8 nt loop structure. Dr Kim presented evidence that mono-uridylation promotes Dicer processing and a significant part of the talk after that has focused on which TUTase are in charge for the above process. Tut-7 was found to be the major enzyme for this at least in Hela cells.

Regulatory RNA in Human Development and Disease,

Dr. John Mattick, Garvan Institute of Medical Research

Dr Mattick’s talk initially included an excellent  overview of the state of the art in the field of regulatory non-coding RNAs. Starting with the question where is the information for complexity in higher eukaryotes  encoded he presented key findings from the FANTOM consortium and subsequent works of his Lab.

Among them he talked on how distinct sets of lncRNAs are expressed in a tissue-development specific manner and pointed out to  the low ncRNA expression levels observed due to this specificity and the small number of cells in populations tested. To this end he showed examples (from hippocampus tissue and other tissues) on why rear expression of many non-coding RNAs means specific expression and should not be underestimated.

Instead, as he showed with his findings employing  the ultra-sensitive RNA capture seq  transcription can be identified in gene deserts as well as  splicing. For example, this approach led to identification of novel Hox transcripts as well as new p53 isoforms hidden by predominant isoforms. On the last part of his talk Dr Mattick referred to GWAS and the finding that most of disease associated loci occur in non-coding regions.  To this end a custom RNA capture seq array to target 150 disorders  was employed.

Epigenetic Genome Control by Heterochromatin and RNAi Machinery,

Shiv Grewal, NCI, NIH

Dr Grewal presented his recent findings on the role of RNAi in heterochromatin formation.  Initially, Dr Grewal referred to previous works of his lab on the way RNAi silences centromeric repeats.  Here, he made one step further and asked whether similar effects can be observed elsewhere in the genome. Interestingly, he showed that siRNA clusters and RNAi dependent heterochromatin assembly emerge also in gene containing regions upon disruption of exosome.

Moreover, these regions responded with an increase in  H3K9me2.  Among the example regions he showed was the Tf2 retrotransposon. Subsequently, Dr Grewal presented data showing how RNAi and heterochromatin modifiers work together in a coordinated fashion that actually overlaps each other. To this end, he unfolded further a mechanistic model in which transcripts are recognized by Pla1 and Pab2 in a  mechanism involving Red 1 and yet unknown factors in response to environmental stimuli. As he noted at the end of his talk, there is certainly more to be revealed in the future regarding the interaction between RNA processing and silencing.

lncRNA Poster Sessions

A remarkable characteristic of this meeting compared to many previous ones in this field was the explosion in the number of long non-coding  RNAs that were tested in terms of function. As noted above, instead of just describing and cataloging new lncRNAs many groups presented functional assays addressing the role of these lncRNAs in epigenetic regulation during developmental decisions and stem cell differentiation.  Another significant part focused also on the control of these lncRNAs on cell cycle progression, especially in terms of cancer progression.

Concluding Remarks Noncoding RNAs in Development and Cancer 

Perhaps the most interesting aspect of the conference beside getting an update on what is hot at the moment in the field was the great range of the information the attendants were exposed to, from procaryotes and yeast to mouse and human, from basic biochemistry and structural aspects to computational, genomic and clinical issues, revealing that the field remains still a vibrant yet unknown area to be approached in a rather inter- and multidisciplinary way.

EpiGenie would like to thank Dr. Athanasios Zovoilis of Harvard Medical School for his great coverage of this event.