1. Xiaole Shirley Liu STAT115, STAT215, BIO298, BIST520
lncRNA
Xiaole Shirley Liu
STAT115, STAT215, BIO298, BIST520

2. Outline Last lecture, short non-coding RNAs: miRNA, siRNA, piRNA
Today: long non-coding RNAs (lncRNAs)
Systematically discovery of lncRNA
Function of lncRNA

3. 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

4. RNA-seq Mostly not investigated on microarrays before
Many LncRNAs are spliced and have intervening expression pattern with coding
genes

5. 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

6. lncRNA Signaling Xist and X-inactivation
In vertebrate genomes, male has XY, female has XX but only one of the X is active

7. lncRNA as miRNA Decoy
Poliseno et al, Nat 2011

8. LincRNA as Scaffold for Transcription Repression
HOTAIR and PRC2
Tsai et al, Science 2010

9. Map lncRNAs Associated with Chromatin Factors
Many chromatin factors have RNA-binding domains, functions modulated by lncRNA
RIP-seq of chromatin factors
Downstream analysis?

10. Map lncRNA Occupancy
ChIRP: Chromatin Isolation by RNA Purification (ChIRP)
Chu et al, Mol Cell 2011

11. Upstream Antisense RNA
Pervasive upstream antisense RNA
Core et al, Science 2008

12. Enhancer RNA
Weak level of Pol II and RNA transcripts observed at distal TF binding sites
Kim et al, Nat 2010

13. LincRNA as Enhancers Some LincRNAs promote nearby gene trx
Orom et al, Cell 2010

14. Potential Functions of lncRNAs

16. 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

17. 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 … goals

18. 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

19. 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

20. How to Write a Specific Aims Page
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