LncRNA Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520.

lncRNA

Xiaole Shirley Liu

STAT115, STAT215, BIO298, BIST520

Outline

• Last lecture, short non-coding RNAs: miRNA, siRNA, piRNA

• Today: long non-coding RNAs (lncRNAs)• Systematically discovery of lncRNA• Function of lncRNA

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ChIP-seq

• lncRNA are mostly polII transcribed, and has similar histone mark profiles as protein-coding genes.

• Guttman et al, Nat 2009 use active promoter and Pol2 elongation mark to find lncRNAs, know the TSS and direction of transcription

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RNA-seq

• Mostly not investigated on microarrays before

• Many LncRNAs are spliced and have intervening expression pattern with coding

genes

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LncRNA Functions

• Similar to coding RNAs, lncRNA is transcribed by pol2, regulated by TFs, and have polyA tails

• Expression levels of lncRNA is often lower than coding RNAs

• Gradually finding very important functions of some lncRNAs, some overlapping functions

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lncRNA Signaling

• Xist and X-inactivation

• In vertebrate genomes, male has XY, female has XX but only one of the X is active

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lncRNA as miRNA Decoy

• Poliseno et al, Nat 2011

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LincRNA as Scaffold for Transcription Repression

• HOTAIR and PRC2

Tsai et al, Science 20108

Map lncRNAs Associated with Chromatin Factors

• Many chromatin factors have RNA-binding domains, functions modulated by lncRNA

• RIP-seq of chromatin factors

• Downstream analysis?9

Map lncRNA Occupancy

• ChIRP: Chromatin Isolation by RNA Purification (ChIRP)

• Chu et al, Mol Cell 2011

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Upstream Antisense RNA

• Pervasive upstream antisense RNA

Core et al, Science 200811

Enhancer RNA

• Weak level of Pol II and RNA transcripts observed at distal TF binding sites

Kim et al, Nat 201012

LincRNA as Enhancers

• Some LincRNAs promote nearby gene trx

Orom et al, Cell 201013

Potential Functions of lncRNAs

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Summary

• Pervasive ncRNA transcripts exist in the genome, carrying diverse functions from epigenetic, co-transcriptional, and post-transcriptional regulatory roles

• NGS enables the discovery and better understanding of these ncRNA and their mechanisms

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Grant Proposal: Specific Aims

• Grant title and your name

• Introductory paragraph (~1/4 page)– A is very important in bio/medicine/disease– Recent development in A has made some really

significant findings or improvements– However, something is still lacking or not

known about A– The central hypothesis of this proposal is …– Therefore, we plan to do investigate / develop

… for … goals17

How to Write a Specific Aims Page

• Specific Aims (1/3 to ½ page)– To achieve the goals, we plan to:– Aim 1: profile the genome-wide xxx of xxx

• 1.1: establish xxx

• 1.2

– Aim 2: develop a computer algorithm or knowledge base

• 2.1: model xxx

• …

– Aim 3: identify the mechanism of xxx• …

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Specific Aims

• Sound like you can definitely do it• Do not use words that sounds like a fishing

expedition such as try, explore (find) or words that sound too trivial such as download (integrate)

• Try not to let your aims depend on each other• Propose as many aims as years for the grant

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• Last paragraph (< ¼ page)– What’s novel about our approach– Deliverables (what will the scientific

community see at the end)• A software, database, map, mechanism, resource

– What’s the (potential) significance about our proposal

• Best possible outcome

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How to Write a Specific Aims Page