Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions...
-
Upload
marylou-mclaughlin -
Category
Documents
-
view
293 -
download
67
Transcript of Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions...
![Page 1: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/1.jpg)
Non-coding RNA
![Page 2: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/2.jpg)
What is noncoding RNA?
Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein
![Page 3: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/3.jpg)
How many RNAs in cells ?
mRNA
rRNA
tRNA
Protein
snRNA
snoRNA
gRNA
Antisense RNA
SRP-RNA
microRNApRNA
Ribozyme
Telomerase RNA
??
![Page 4: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/4.jpg)
Functional diversity of ncRNAs
![Page 5: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/5.jpg)
Scheme for the function of different sncRNAs by targeting bacterial or eukaryal mRNAs or pre-mRNAs leading to regulation of gene expression
The function of diffenent small non-coding RNAs by targeting mRNAs or pre-mRNAs
![Page 6: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/6.jpg)
non-coding RNA (20-20000nt)
RNA
mRNA
small non-coding RNA (sncRNA) (20-500nt)
long non-coding RNA (lncRNA) (>500-20000nt)
![Page 7: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/7.jpg)
Non-coding RNA: Versatility in form and function
Noncoding RNA genes are surprisingly numerous.
Noncoding RNA have a very different functions.
![Page 8: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/8.jpg)
Time for RNomics
![Page 9: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/9.jpg)
Cell, 89: 669–672, May 30, 1997
![Page 10: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/10.jpg)
PNAS, 97(26): 14035-14037, Dec 19, 2000
Understanding RNomics from an expending snoRNA world
![Page 11: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/11.jpg)
Couzin J. Breakthrough of the year. Small RNAs make big splash.
Science. 2002 Dec 20;298(5602):2296-7.
![Page 12: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/12.jpg)
DNA RNA Protein
Study non-coding RNAs on the genomic scale
Study the identification, expression, biogenesis, structure, regulation of expression, targets, and biological functions of noncoding RNAs on the genomic scale.
![Page 13: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/13.jpg)
sncRNAs are very small
sncRNAs contain no specific features at their
5’ and 3’ ends
How to identify the ncRNA genes in genomic studies?
![Page 14: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/14.jpg)
methods for finding novel non-coding RNA genes
Computational RNomics Searching conserved intronic sequences by comparative analysis of
introns
Searching conserved intergenic sequences
Searching well-defined sequence elements or characteristics (boxC/D,
functional regions, complementary and other conserved sequence etc.)
Novel algorithm taking the folding parameters in RNA molecule into
account
All predictions of novel ncRNA genes need to be confirmed by direct detection of these transcripts !!!
![Page 15: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/15.jpg)
A Computational Screen for Methylation Guide snoRNAs
SCIENCE, 283: 1168-1171, FEBRUARY 19, 1999
A example of computational approach for screening box C/D snoRNAs
![Page 16: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/16.jpg)
Similarity Searching
Proteins BLAST, Sequence Alignment Genes that code for proteins are conserved
across genomes (e.g. low rate of mutation) ncRNA
Secondary structure usually conserved Alignment scoring based on structure is im
perative
![Page 17: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/17.jpg)
orthologous ( a1 in species I, a1 in species II)
paralogous ( a1 and a2 in species I )
Orthologous and paralogous
![Page 18: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/18.jpg)
Repeat Sequence
repeat sequence
Inverted repeat, palindrome sequence
mirror repeat
![Page 19: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/19.jpg)
(Inverted repeat)
G A A T T C
C T T A A G
![Page 20: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/20.jpg)
![Page 21: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/21.jpg)
![Page 22: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/22.jpg)
Triple helix
![Page 23: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/23.jpg)
ncRNA: Sequence vs Structure
![Page 24: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/24.jpg)
The specificity of RNA search
ncRNA is defined by
primary and secondary structure
![Page 25: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/25.jpg)
RNA structure
Base-pairing defines a secondary structure
![Page 26: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/26.jpg)
RNA is extremely difficult to crystallize:
RNA is enzymatically unstable molecule (RNAses are
everywhere!)
RNA is conformationally flexible molecule.
Thus Bioinformatic approach –
RNA structure prediction is very important !
Tertiary stuctures are much less well understood
![Page 27: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/27.jpg)
L-shaped tRNA molecule
![Page 28: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/28.jpg)
methods for finding novel non-coding RNA genes
Traditional methods
by PAGE separation of non-coding RNAs and sequencing
by immunoprecipitation of specific RNPs
by non-coding RNA enriched cDNA libraries and sequencing
by microarray analysis
New
new method
by non-coding RNA libraries and deep sequencing
Experimental RNomics
![Page 29: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/29.jpg)
Deep sequencing
![Page 30: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/30.jpg)
Functional analysis
Combination of bioinformatical methods and experimental methods in ncRNA functional analysis
structure and functional analysis
Computational Analysis
Functional Prediction
Structural
Prediction
Functional Analysis by Experimental Method
![Page 31: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/31.jpg)
Nomenclature of non-coding RNA
Bacterial RNAs --- Small RNA(sRNA) Eukaryotic RNA --- Non-coding RNA (ncRNA),
functional RNA (fRNA), small nonmessenger
RNAs (snmRNA) Based on subcellular localization ---
Small nucleolar RNAs (snoRNA) Based on size --- micro RNA (miRNA) , small
interfering RNAs (siRNA), long non-coding
RNA(lnRNA)
![Page 32: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/32.jpg)
Box C/D and box H/ACA guide snoRNAs and the core associated proteins
snoRNA
![Page 33: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/33.jpg)
methyl groups or pseudouridine groups
methylation and pseudouridylation guided by snoRNAs
RNA processing and modification
![Page 34: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/34.jpg)
Box C/D snoRNA
(a) (b)
Box C/D snoRNAs direct rRNA methylation
![Page 35: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/35.jpg)
Box H/ACA snoRNA
(a) (b)
Box H/ACA snoRNAs direct rRNA pseudouridylation
![Page 36: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/36.jpg)
Box C/D-H/ACA snoRNA (scaRNA)
![Page 37: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/37.jpg)
snoRNA target
snoRNA --------------------------------------rRNA, U6
scaRNA---------------------------------------snRNA
imprinted snoRNA------ -------------------mRNA
Homologs of snoRNAs in Archaea-----rRNA and tRNA
Orphan guide snoRNAs-------------------No target
![Page 38: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/38.jpg)
(1)
(2)
(3)
(4)
Diversity of genomic organization of ncRNAs
Trends Plant Science, 8(1): 42-49, 2003
snoRNA gnene organization
![Page 39: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/39.jpg)
Diversity of genomic organization of ncRNAs
microRNA gnene organization
![Page 40: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/40.jpg)
Diversity of genomic organization of ncRNAs
![Page 41: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/41.jpg)
snoRNA and microRNA gene cluster
![Page 42: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/42.jpg)
Polycistronic and intronic pre-snoRNA transcripts are processed by either a splicing or a non-splicing pathway
Procession of polycistronic and intronic pre-snoRNA transcripts
![Page 43: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/43.jpg)
Non-coding RNA host gene
Protein Coding Gene------Most intronic snoRNA genes of vertebrates and yeast are nested in genes encoding proteins involved in ribosome biogenesis.
Non-coding RNA gene------These ‘‘host’’ genes harbour snoRNAs in multiple introns but their exon does not code for proteins
![Page 44: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/44.jpg)
SPAC1B3.05 snR80 snR90 SPAC1B3.05
Exon 2 Intron Exon 1
snR90 precursor
snR80
Nucleases
Intron lariat
Splicing
Exonuclease trimming
snR90
snR80 snR90
Exon 2 Intron Exon 1
Polycistronic precursor
Transcription
![Page 45: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/45.jpg)
microRNA
![Page 46: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/46.jpg)
The discovery of miRNAs
• miRNA was first discovered in 1993 by Victor Ambros at miRNA was first discovered in 1993 by Victor Ambros at Harvard (Harvard (lin-4lin-4))• The second miRNA The second miRNA Let-7Let-7 was discovered in 2000 by Frank was discovered in 2000 by Frank Slack as a postdoc at HarvardSlack as a postdoc at Harvard (Ruvkun lab)(Ruvkun lab)
Victor AmbrosVictor Ambros Gary Ruvkun
![Page 47: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/47.jpg)
The first discovered miRNA The first discovered miRNA lin-4 in 1993lin-4 in 1993
Ruvkun G, Wightman B, Ha I. The 20 years it took to recognize the importance of tiny RNAs. Cell. 2004 Jan 23;116 (2 Suppl):S93-6.Lee R, Feinbaum R, Ambros V. A short history of a short RNA. Cell. 2004 Jan 23;116 (2 Suppl):S89-92
Thought to be an oddity not a general phenomenon
![Page 48: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/48.jpg)
Breakthrough with BlastN of the second miRNA (stRNA) let-7
Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P,Davidson E, Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature. 2000 Nov 2;408(6808):86-9.
![Page 49: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/49.jpg)
MicroRNAs: 22-25 nt Noncoding RNAs
Bartel, Cell 116: 281-297, 2004
The foundingmembers
Animals Plants
![Page 50: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/50.jpg)
microRNAs had been neglected for so many years because of their small size.
The underlying reason is: The underlying reason is: people never dream that people never dream that small RNAs will have imsmall RNAs will have important biological roles.portant biological roles.
![Page 51: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/51.jpg)
miRNA biogenesismiRNA biogenesis
Pri-miRNA( 原初 miRNA)
DroshaDrosha(1)(1)
pre-miRNA( 前体 miRNA)
DicerDicer(2)(2)
成熟 miRNA
Exportin 5 (Exp5) transports pre-miRNA to the cytoplasm
![Page 52: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/52.jpg)
Cell 125, 887–901, 2006
![Page 53: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/53.jpg)
Another View
Microprocessor Complex
![Page 54: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/54.jpg)
Differences in miRNA Mode of Action
![Page 55: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/55.jpg)
![Page 56: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/56.jpg)
microRNA nomenclature
Experimentally confirmed microRNAs are given a number that is
attached to the prefix mir followed by a dash eg mir-123.
miRNAs with similar structures bar at 1 or 2 nucleotides are an
notated to show their similar structure with added lower case lette
r eg miR-1a and miR-1b.
miRNAs at different loci to produce the same miRNA and these
are show with additional number eg miR-1-1 and miR-1-2
microRNA nomenclature should also be preceded by the annot
ation for the species they are observed in eg homo sapiens = hsa
-miR-xxx.
![Page 57: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/57.jpg)
Discovery of siRNA
In 1998, the American scientists Andrew Fire and Craig Mello published their discovery :
RNA interference
![Page 58: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/58.jpg)
Andrew Z. FireAndrew Z. FireCraig C. MelloCraig C. MelloAndrew Z. FireAndrew Z. FireCraig C. MelloCraig C. Mello
The Nobel Prize in Physiology or Medicine 2006
![Page 59: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/59.jpg)
siRNA-Mediated Gene Silencing
![Page 60: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/60.jpg)
What is the Difference between miRNA and siRNA?
siRNA originates with dsRNA;
miRNA originates with ssRNA that forms a hairpin
secondary structure.
siRNA is often 100% complementary to the target;
miRNA is often not 100% complementary to the target.
![Page 61: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/61.jpg)
A comparison between miRNA and siRNA
![Page 62: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/62.jpg)
RNAi by siRNAs
processing~22nt
siRNAs
target
recognition
mRNA
degradation
Developmental regulationby MicroRNA
~22ntlin-4
processing
target
recognitionlin-14mRNA
lin-41mRNA
3’UTR
3’UTR
~22ntlet-7
Translational repression
![Page 63: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/63.jpg)
Base Pairing Differences between miRNAs and siRNAs
![Page 64: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/64.jpg)
Transcriptional Gene Silencing by Transcriptional Gene Silencing by Directing Chromatin Modification Directing Chromatin Modification
![Page 65: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/65.jpg)
RNA silencing in different organisms
![Page 66: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/66.jpg)
RNA-Mediated Gene Silencing
Post-transcriptional Gene Silencing (PTGS) or RNA Interference (RNAi)
Transcriptional Gene Silencing (TGS)(RNA-dependent DNA Methylation)
Gene Silencing By MicroRNAs
![Page 67: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/67.jpg)
Transcription from RNAP III promoters of U6 and H1
are well characterized.
RNAP III transcription uses a well-defined termination
signal (TTTTT) and the products have no extra sequence.
Transcription from these promoters is very efficient in
various tissues.
Expression of hairpin RNA (shRNA) usinExpression of hairpin RNA (shRNA) using a Pol III promoterg a Pol III promoter
![Page 68: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/68.jpg)
Vector-based SiRNAplasmid and viral vectors
![Page 69: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/69.jpg)
establishing long-term RNAi:let the cell make the siRNA for you!
![Page 70: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/70.jpg)
Example of Expression Vector
![Page 71: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/71.jpg)
lentiviral construct for siRNAs
![Page 72: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/72.jpg)
siRNA Delivery & Processing
![Page 73: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/73.jpg)
21 世纪初 RNA 研究正在兴起
2000 年世界十大科技突破的第二条
2001 年世界十大科技突破的第二条
2002 年世界科技十大突破的第一条
2004 年世界科技十大突破均来自 RNA
![Page 74: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/74.jpg)
– 种类:主要有 5种 U1 、 U2 、 U4 、 U5 、 U6 ;其它如: U11 、 U12 等
– 功能 :•识别剪接点并与之结合•形成剪接体的三维结构,助于反应进行•可能有催化转酯反应的作用
snRNA snRNA (( small nuclear RNAsmall nuclear RNA ))
是细胞内稳定表达的一类是细胞内稳定表达的一类 RNARNA ,转录后需与多种蛋白子结,转录后需与多种蛋白子结合形成合形成 snRNP(small nuclear ribonucleoprotein particles)snRNP(small nuclear ribonucleoprotein particles)
![Page 75: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/75.jpg)
The Spliceosome Assembly Pathway
U1
U1 U2A
U6
U5U4
U2
U1
U4U6
U5
U2
ATP
E(Commitment Complex)
A(Pre-spliceosome)
B(spliceosome)
C(Activated Spliceosome)
U6
U5
U2mRNA
Exon 1
Exon 1
Exon 2
Exon 2
![Page 76: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/76.jpg)
gRNA RNA editing
in RNA editing, the coding sequence of an mRNA
molecule is altered after transcription, and so t
he protein has an amino acid sequence that dif
fers from that encoded by the gene.
observed in mRNAs, tRNAs, and rRNAs from a wi
de range of organisms;
include the insertion and the deletion of nucleotid
es and the conversion of one base into another
![Page 77: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/77.jpg)
T. brucei ( 布氏锥虫 )gCYB
gRNA 68nt
导致 RNA 编辑中 U 的加入与去除
![Page 78: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/78.jpg)
UUA GGU AUA AAA GUA GAU UGU AUA CCU GGU AGG UGU AAU
L G I K V D C I P G R C N
T TA GGT ATA AAA GTA GA G A A CCT GGT AGG TGT AAT
mRNA 顺序
蛋白质顺序
DNA 正链
480 490 500 510
480 490 500 510
锥虫 COII 基因片段及其表达产物的序列比较
核酸序列的数字是以起始密码子 AUG(ATG) 的 A 开始编码.
![Page 79: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/79.jpg)
The Xist RNA is a large non-coding RNA which has been shown to necessary for developmentally regulated chromosomal silencing in females.
Xist RNA
Human XistRNA 16,500nt X
![Page 80: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/80.jpg)
有丝分裂中失活 X染色体(蓝色)上的 Xist RNA (红色)Cell, 93, 309-312, (1998)
![Page 81: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/81.jpg)
在双链 DNA 病毒增殖和成熟的过程中 , 需要将相当长的子代 DNA 装入一个空间极为有限的新生病毒衣壳中。早在 1987 年 , Guo P X等在对噬菌体ф29 DNA 的转运进行研究时发现了一种具有转运功能的 RNA 分子 , 该 RNA分子在噬菌体ф29 的 DNA 包装中有着重要的作用 , 这种 RNA 分子被称为 pRNA(packaging RNA) 。
pRNA
![Page 82: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/82.jpg)
pRNA
![Page 83: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/83.jpg)
![Page 84: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/84.jpg)
人 端粒 RNA( 451nt)
端粒 (telomere) 是真核细胞染色体的生理性末端,由高含 G 的 DNA 序列和相应的蛋白组成。
端粒的维持需端粒酶 (telomerase) 的激活。端粒酶是一种核糖 - 核蛋白复合体,其中 RNA 和蛋白质是端粒 DNA 合成所必须的。它不同于经典的 DNA 聚合酶,而是专一的逆转录酶,能以自身的 RNA 为模板,逆转录合成端粒 DNA ,以补偿细胞分裂时染色体末端缩短 .
![Page 85: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/85.jpg)
Telomerase RNA • Component of telomerase
• Provides template for telomere synthesis
• Role in Cancer and Aging
![Page 86: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/86.jpg)
Telomerase a reverse transcriptase to elongate telomeric DNA
RNA
Protein
’3 5’
C A A U C C C A A U C
G G G T T
(AATCCC)n
A
5’3’
(TTAGGG)n
dATPdTTP
dG
TP
![Page 87: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/87.jpg)
RNA
’3 5’
C A A U C C C A A U C
G G G T T
(AATCCC)n
A
5’
(TTAGGG)n
A G G G T T3’
Telomerase a reverse transcriptase to elongate telomeric DNA
![Page 88: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/88.jpg)
RNA
’3 5’
C A A U C C C A A U C
G G G T T
(AATCCC)n
A
5’
(TTAGGG)n
A G G G T T3’
Telomerase a reverse transcriptase to elongate telomeric DNA
![Page 89: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/89.jpg)
RNA
’3 5’
C A A U C C C A A U C
G G G T T
(AATCCC)n
A
5’
(TTAGGG)n
A G G G T T3’
Telomerase a reverse transcriptase to elongate telomeric DNA
![Page 90: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/90.jpg)
RNA
’3 5’
C A A U C C C A A U C
G G G T T
(AATCCC)n
A
5’
(TTAGGG)n
A G G G T T A G G G T T3’
Telomerase a reverse transcriptase to elongate telomeric DNA
![Page 91: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/91.jpg)
RNA
’3 5’
C A A U C C C A A U C
G G G T T
(AATCCC)n
A
5’
(TTAGGG)n
A G G G T T A G G G T T3’
Telomerase a reverse transcriptase to elongate telomeric DNA
![Page 92: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/92.jpg)
DNA polymerase
G G G T T
(AATCCC)n
A
5’
(TTAGGG)n
A G G G T T A G G G T T
primer3’
Telomerase a reverse transcriptase to elongate telomeric DNA
![Page 93: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/93.jpg)
A myriad of RNAs and functional diversity
mRNA, tRNA, rRNA: protein biosynthesis
gRNA: mRNA editing snRNA: mRNA processing (splicing and maturation) snoRNA: rRNA processing( cleavage and modification) RNA P: tRNA processing Telomerase RNA: DNA replication and life SRP-RNA: transport miRNA: regulation of gene expression in transcription and post-transcription levels siRNA: gene silence Xist and Tsix: X chromosome inactivation
……
![Page 94: Non-coding RNA. What is noncoding RNA? Non-coding RNA (ncRNA) is a RNA molecule that functions without being translated into a protein.](https://reader035.fdocuments.net/reader035/viewer/2022062718/56649eb45503460f94bbd159/html5/thumbnails/94.jpg)
a hidden “RNA world”
within modern DNA world