W9L2 eRNA, circRNA Flashcards
Problem with standard RNA-sequencing
Identifies steady state RNA present in a cell/tissue
* Will not identify transcripts lacking poly(A) tail if using poly(A) enrichment
* May not identify rare RNA or those with short half life
* Will not identify RNA with modifications that interfere with reverse transcription or adaptor ligation
Problem with measuring RNA transcript
Steady state levels of RNA do not accurately mirror transcriptional activity
RNA abundance determined by numerous factors – processing efficiency, RNA stability, miRNA activity
Nuclear run-on experiments map sites in the genome that are transcriptionally engaged
Nuclear run on assay
- Isolate nuclei and pause transcription (ice incubation)
- Introduce a nucleic acid label( Br-UTP run on)
- Restart transcription
- Isolate nascent transcripts and sequence using immunoprecepitation
Global run-on sequencing (Gro-seq) results
Find that transcription occurs upstream of the annotated TSS
Some genes have a peak of transcription at the Transcription Start Site
RNA pol II pausing
Peak of seq reads seen at some TSS is due to pausing of RNA pol II
-30% of human gene are paused. Much lower transcript than initial binding to the TSS
-New way of gene regulation: pausing of RNA elongation by regulatory protein (NELF)
Small RNAs arise from enhancer
Study of mouse neuronal enhancers revealed 1000s bound by RNA pol II and bi-directionally transcribed
Mapping TSS of expressed regions of the human genome
-Study of human cell types and tissues revealed 43K enhancers bound by RNA pol II and bi-directionally transcribed
Characteristic of eRNAs
2D-eRNAs (200bp-2kb)
§ Bidirectional transcription at a high rate
§ Short-lived (half-life = minutes)
§ Capped, non-polyadenylated, non-spliced
§ Function in cis
1D-eRNAs (enhancer-associated lncRNAs) (4-5kb)
§ Unidirectional transcription
§ Longer-lived
§ Capped, polyadenylated, spliced
§ Can function in cis or trans
Possible roles for eRNAs
There are two possible roles for eRNAs
1. eRNA synthesis facilitates delivery of RNA pol II to corresponding promoter by tracking along the DNA between the enhancer and TSS
2. eRNAs themselves or their transcription allows enhancers to adopt an open chromatin configuration required for gene activation
Testing the eRNA transfer fuction
Placing transcription termination sequence between eRNA and target gene should block the transfer of RNA pol II
Issues with tracking model
eRNAs do not originate between the enhancer and TTS of associated gene
RNA pol II is delivered to TSS via DNA looping – eRNAs stabilise interactions between DNA and cohesion/mediator
Idea of open chromatin and eRNA
Enhancer in a closed chromatin state – enhancer inactive + gene inactive
Transcription at enhancer promotes an open chromatin state – enhancer becomes active
Enhancer promotes transcription of gene
Enhancer in a closed chromatin state – enhancer inactive
Block transcription elongation Histone marks not deposited Enhancer remains inactive
eRNAs interact with chromatin modifiers
eRNAs promote activity of CREB-binding protein (CBP) leading to increased acetylation of surrounding histone tails (open configuration)
Transcriptional activation via changes in chromatin landscape –enhancer/promoter
Interactions between eRNAs and chromatin modifying factors is non specific
eRNAs interact with transcriptional co-activators
eRNAs interact with bromodomain of co-activator BRD4 and both enhance and stabilize binding to nearby acetylation marks – maintains enhancer and gene activation
BRD4 binding to eRNA is locus specific – associates only with BRD4-bound enhancers - cis regulation
eRNA maintain the transcription factor
eRNAs capture disassociating transcription factors to enhance their occupancy at enhancers (TF trapping)
Generates a positive-feedback loop in which TFs stimulate local enhancer transcription, which increases occupancy – increases and stabilises gene expression
eRNA and decoy
eRNAs promote RNAPII pause release by acting as a decoy for the negative elongation factor (NELF) and by activating positive elongation factor P-TEFb
How much circular RNA are in us
1000s of circular RNAs in human and mouse tissues, and in different developmental stages of the nematode worm
-abnormal exon structure
-occur due to gene can be canonical linear splicing or blacksplicing
Canonical linear splicing
Upstream 3’ splice site is covalently linked to a downstream 5’ splice site
Backsplicing
circRNA features
circRNAs lack poly(A) tails and 5’ Cap – usually 100nt (spliced)
May contain a single exon, several exons as well as introns
Non-coding – as cannot recruit eIF4F complex/PIC
Very stable with long half-life
Found in animals (metazoan and single-celled) and plants
Diverse fuction of CircRNA
-sponging miRNA
-interacting with RBP
-regulating transcription
-regulating splicing
-translated into protein
-regulating Epigenetic alteration
ciRS-7 circRNA is immune to miRNA-mediated degradation
-ciRS-7 in human and mouse brains has 74 conserved binding sites for miR-7
-Linear + polyadenylated ciRS-7 (ciRS-7-fs) is susceptible to miR-7 degradation but circular ciRS-7 is stable
ciRS-7 and miR-7 expression
If ciRS-7 regulates miRNAs it needs to be co-expressed in the same cells
RNA in situ hybridisation of ciRS-7 and miR-7 in mouse brain sections shows they are co-expressed in the neocortical and hippocampal neurons
ciRS-7 specifically interacts with miR-7
-Immunoprecipitation of tagged-AGO2 from transfected human HEK293 cells
-ciRS-7 pulled down with miR-7/AGO2
Showed that it cannot be degraded
ciRS-7 over-expression in zebrafish
Introduce miR-7 morpholinos into zebrafish
Reduced brain size when miR-7 activity is reduced
Reduced brain size when ciRS-7 is over-expressed
Features of circRNAs that make effective miRNA sponges
- circRNAs are more stable than linear transcripts
- circRNAs are immune to RISC-induced RNA decay through deadenylation
- RISC remain attached to the circRNA
Dynamics of miRNAs and their targets
Top 10 expressed miRNA make up the majority of all miRNAs
Number of predicted miRNA target sites for each miRNA outnumber the abundance of the miRNA
Not clear whether sponges will have much of an effect under normal physiological conditions
-spong does not have much effect on heavily expressed miRNA
-more likely for miRNA to bump into target mRNA than the sponge due to large number of target transcript
ciRS-7 is a target for miR-671
ciRS-7 has near perfect complementarity to miR-671 (like plant RISC)
Northern blot with RNA from HEK293 cells co- transfected with miRNA and ciRS-7 showed that ciRS7 is sliced
Evidence that some mirnA slice their target
