L30 Long non-coding RNA Flashcards
Features of long non-coding RNAs (lncRNAs)
see onenote
- regulate gene activity
- vast majority have no known function
Proposed function of lncRNA
see onenote
Function of lncRNAs - tethers
see onenote
- lncRNA remains tethered to the encoding locus during transcription
- protein binding motif at 5’ end recruits DNA/histone modifying enzymes
- modify chromatin of adjacent sites on the same chromosome, regulation occurs in cis
Function of lncRNAs - guides
see onenote
- lncRNA released from site of transcription
- regulation in cis or trans
Hox gene regulation example
see onenote
multiple lncRNA present in hox clusters
targeted knockout of hotair gene led to homeotic conversion of lumbar to sacral region
Hotair regulates chromatin state
see onenote
hotair functions as a guide in trans
- promotes repressive chromatin state in trans
Hotair - global regulator of gene expression
regulates many other genes, not sequence specific
ecotopic hotair detected in some human cancers - associated with metastasis/progression
- repressive chromatin is lost from transcriptional start sites of upregulated genes
X chromosome inactivation
see onenote
Female calico cats are mosaics
see onenote
x inactivation results in two populations of cells expressing different fur pigmentation - only in heterozygous females
Stages of random XCI in mammals
see onenote
Once embryo becomes implanted in utero => two clonal populations that represent different x inactivated chromosomes
XCI associated with heterochromatin formation
- X selected for silencing (Xi) is coated in lncRNA called Xist
- Xi condenses to form heterochromatin and recruits histone variants
- fully condensed Xi (Barr body) migrates to nuclear periphery
- majority of X-linked genes silenced but a few remain active
X-inactivation centre (XIC)
see onenote
- <500kb region
- source of seven different lncRNA e.g. Xist, Tsix, Xite _ small ncRNAs
- > 7 lncRNA ensure orderly progression through XCI - all are involved in regulating Xist
Xist - X inactive specific transcript
see onenote slides
- 17kb, spliced, polyA non-coding transcript
- constrained to nucleus
- initially expressed at low levels from both X chromosomes in undifferentiated embryonic cells
Xist acts as cis guide
see onenote
Xis lncRNA has many repeat motifs
E.g.
Xist interacts with SPEN, binds to histone deactylase => removes histone activation mark from histone tails
Xist triggers chromatin modification
- PCR2 recruited to Xi by unknown mechanism
- deposit H3K27me3 and other silencing marks
- extensive CG methylation in gene promoters
Secondary chromatin modification
see onenote
Chromosome wide silencing not sufficient for x inactivation, needs further recruitment of chromatin modifying factors - secondary silencing factors that recognised the silenced chromosome, binds to it and causes further formation of heterochromatin
lncRNA controls Xist activity
see onenote
- 40kb antisense Tsix transcript has motifs that are also bound by chromatin modifying factors (CMF) - acts as decoy to control Xist activity in cis
Choosing the X chromosome to be activated
see onenote
- first event in XCI involves brief pairing between X chromosomes
- involves Tsix lncRNA physically interacting with protein to form a protein-RNA bridge
X-X pairing and establishment of Xi
Paired X chromosomes exchange bound
- bound factors accumulate on just one X chromsome (future Xa)
- The one without the activation factors lose tsix expression and will become the inactivated x chromsome
Distribution of bound factors determines Tsix expression
- chromosome lacking bound factors (future Xi) - Tsix no longer expressed, increase in repressive H3k7me marks, Xist expression elevated
