Intro to non-coding RNA

Carmit Levy

I-CORE workshop "Exploring the non-coding RNAs: lncRNA, microRNA, eRNA and circular RNA“

March, 2015

5%–10% of the genome is transcribed 1% encodes proteins

Non Coding RNA:

Housekeeping noncoding RNAs (usually expressed constitutively) • Transfer RNA (tRNA) • Ribosomal RNA (rRNA) • Splicing • small nuclear RNAs Regulatory noncoding RNAs Short • microRNAs • small interfering RNAs • Piwi-associated RNAs Long >200bp • lncRNAs

back to back 1993

Pasquinelli et al., 2005

microRNAs

Non-canonical pathways of miRNA biogenesis

Narry Kim Nature reviews 2014

P-bodies

Mechanisms of miRNA-mediated gene regulation

Direct Indirect

Giovanni, Nature 2008

AGO

P-bodies localization Short interfering RNAs trigger

histone silencing marks Mariano current biology 2010

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Types of Regulation:

3. Gene regulated by microRNA

2. Post transcriptionally

1. Transcriptionally

An example: the study of microRNA

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4. microRNA genomic location

intronic

intergenic

1. miRNA transcriptional regulation

Gaur A. et al, Cancer research March 2007

2. microRNA Post transcriptional regulation

Narry Kim Nature reviews 2014

Obernosterer, RNA 2006

3. miRNA Post- Transcriptional Regulation Tissue specific biogenesis

Bell et al JID 2013

3. Gene regulated by microRNA

Steven G Chaulk 2011 RNA

4. microRNA genomic location

Intronic miR-211 Assumes the Tumor Suppressive Function of Its Host Gene in Melanoma

Levy and Khaled Mol Cell 2011

Methods in miRNA studying

• Real time PCR • In situ hybridization • Small RNA seq • Computational – predicted target

CLIP (cross-linking immunoprecipitation)

miRBase

Non Coding RNA:

Housekeeping noncoding RNAs (usually expressed constitutively) • Transfer RNA (tRNA) • Ribosomal RNA (rRNA) • Splicing • small nuclear RNAs Regulatory noncoding RNAs Short • microRNAs • small interfering RNAs • Piwi-associated RNAs Long >200bp • lncRNAs

lncRNA • 200nt< lncRNA

• may be located within nuclear or cytosolic fractions, may or may not be polyadenylated

• Can be transcribe as:

(1) sense(2) antisense (3) bidirectional (4) or (5)

intergenic

• Database providing expression and information on mammalian lncRNA - Dinger et al., 2009

• Evolutionary studies initiated (2004, 2006)

• First evidance for lncRNA gene that is critical for the X-chromosome inactivation in mammals. 2008

Highly Specific Expression Mouse Brain Ponting, Cell, 2009

lncRNAs are not transcriptional noise

John R. Prensner Cancer Discovery 2011

Gene expression regulation by lncRNA

Mechanisms of lncRNA function

John R. Prensner Cancer Discovery 2011

microRNA sponge

2007

Circular RNAs are a large class of animal RNAs with regulatory potency

Nikolaus Rajewsky, Nature 2013