Annual Scientific Report 2015

Enright Group
Functional Genomics and
Analysis of Small RNA Function
Complete genome sequencing projects are generating enormous amounts of data,
and while progress has been rapid a significant proportion of genes in any given
genome are either un-annotated or possess a poorly characterised function. Our
group aims to predict and describe the functions of genes, proteins and regulatory
RNAs as well as their interactions in living organisms.
Regulatory RNAs have recently entered the limelight
as the roles of a number of novel classes of non-coding
RNAs have been uncovered. Our work involves the
development of algorithms, protocols and datasets for
functional genomics. We focus on determining the
functions of regulatory RNAs, including microRNAs,
piwiRNAs and long non-coding RNAs. We collaborate
extensively with experimental laboratories on
commissioning experiments and analysing experimental
data. Some laboratory members take advantage of these
close collaborations to gain hands-on experience in the
wet lab.
Major achievements
Long non-coding RNAs
Working closely with the Furlong group at EMBL
Heidelberg and the O’Carroll group at the University
of Edinburgh, we explored the roles of long non-coding
RNAs in different systems. Through extensive, deep
sequencing in mouse, we identified a catalogue of
lncRNAs expressed through the murine germline. From
this incredibly detailed atlas of transcription, we began
to identify a set of lncRNAs whose functions may be
extremely important to the maintenance of the germline
and genomic integrity. With the Furlong group we began
exploring the roles of lncRNAs in the development of
the mesoderm in D. melanogaster embryos, and
developed a range of new pipelines and techniques that
greatly improved our ability to delineate real transcripts
from artefacts and DNA contamination accurately.
Current results are extremely encouraging, showing
that we have discovered many novel lncRNAs with very
specific and interesting expression patterns according to
in situ hybridisation.
We performed two experiments in collaboration with
the Mattick Lab at the Garvan Institute, Australia,
exploring the use of a probe-based sequencing
technology (i.e. CaptureSeq) in both human and mouse
genomes, illustrating the tremendous complexity of the
transcriptome in both species. This novel approach uses
probes designed around transcript isoforms to perform
extremely deep sequencing targeted at deciphering the
appropriate transcript assembly for mRNAs or lncRNAs
of interest.
We worked with the laboratory of Tony Kouzarides at
the Gurdon Institute in Cambridge to explore a class of
lncRNAs which show conserved syntenic signatures
between Human and Mouse. These positionally
conserved RNAs appear to be essential to the function
and expression of their neighbouring protein-coding
genes and we are working closely with the Kouzarides
lab to further isolate their specific biochemical or
structural functions.
Clinical genomics
In our long-standing collaboration with the Department
of Pathology at the University of Cambridge and
Addenbrooke’s Hospital, we previously explored the
roles of microRNAs and other non-coding RNAs in
paediatric germ cell tumours and solid tumours such
as neuroblastoma. In 2015 we focused on the analysis
of Human Papilloma Virus (HPV) integration sites
in human cervical cell lines to explore how HPV
integration leads to oncogenesis. This work involved
large-scale RNA-seq, DNA sequencing and targeted HiC
analysis to explore where in the genome HPV integrates
across a clonal set of cervical cells and the effects that
this integration has on gene-expression. We hope that
this on-going work will shed light onto viral oncogenesis
and cervical cancer.
a)
b)
phyloP score
phyloP score
-20 bp 5p
-20 bp 3p
coding
non-coding
20 bp
coding
non-coding
20 bp
Analysis of spice site donor/acceptor conservation in coding versus noncoding
sequences based on the CaptureSeq technology for extremely deep
sequencing and isoform quantitation/discovery.
c)
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2015 EMBL-EBI Annual Scientific Report