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Joint Research Seminar (24 Feb 2015)

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Joint Research Seminar

Genomics Strategic Research Theme
Centre for Genomic Sciences

Characterization of Novel Noncoding RNAs
by Integrating High-throughput Data with
Secondary Structure Prediction

Dr Zhi John LU

School of Life Science
Tsinghua University


24 February 2015 (Tue)
3:00 – 4:00pm


Seminar Room 2
G/F, HKJC Building for Interdisciplinary Research

5 Sassoon Road, Pokfulam, HK

 
Abstract:

I will present an integrative method for whole-genome identification and characterization of novel non-coding RNAs (ncRNAs), which has been applied to model genomes studied by ENCODE and modENCODE projects. To find signature features shared by various ncRNA sub-types and characterize novel ncRNAs, we have developed a method, RNAfeature, to investigate >600 sets of genomic and epigenomic data with various evolutionary and biophysical scores. RNAfeature utilizes a fine-tuned intra-species wrapper algorithm that is followed by a novel feature selection strategy across species. It considers long distance effect of certain features (e.g. histone modification at the promoter region). We finally narrow down on 10 informative features (including sequences, structures, expression profiles and epigenetic signals). These features are complementary to each other and as a whole can accurately distinguish canonical ncRNAs from CDSs and UTRs (accuracies: >92% in human, mouse, worm and fly). Moreover, the feature pattern is conserved across multiple species. For instance, the supervised 10-feature model derived from animal species can predict ncRNAs in Arabidopsis (accuracy: 82%). Subsequently, we integrate the 10 features to define a set of noncoding potential scores, which can identify, evaluate and characterize novel noncoding RNAs. The score covers all transcribed regions (including unconserved ncRNAs), without requiring assembly of the full-length transcripts. Importantly, the noncoding potential allows us to identify and characterize potential functional domains with feature patterns similar to canonical ncRNAs (e.g. tRNA, snRNA, miRNA, etc) on 70% of human long ncRNAs (lncRNAs).
 

ALL ARE WELCOME


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