lncRNAs

long,non-codingRNAs

MainlytranscribedbyRNAPol II

CharacteristicsoflncRNAs

Nuclearand/orcytoplasmaticlocaliztion

DBE-T

lncRNAsinphysiology

COMPARINGmRNAs- lncRNAs

COMPARINGmRNAs- lncRNAs

lncRNAscanbe1. Intergenic (lincRNA):Donotintersectwithproteincodinggene

2.Genic:Intersectaproteincodinggene- Exonic- Intronic- overlapping

Divergent

Convergent

samestrandP P

P

PP

P

Closest protein coding gene lncRNAP:promoter Why? Why? Why?

COMPARINGmRNAs- lncRNAs

A.LncRNAsdonothavecodingpotential:à LongestpossibleORFwassearchedinmRNA/lncRNAs

B.CAGEtagscanbefoundinlncRNAsà definedtranscriptionalstartsiteCAGEtagfreqeuncy increaseswithincreasedlncRNAexpressionlevels.mRNAsarecharacterizedbymoreCAGEtagsà LncRNAsaresimilartomRNAs

CAGE

freqeuncy

Expressionlevels

COMPARINGmRNAs- lncRNAs

SPLICING:- 98%oflncRNAsarespliced,- RelevantSplice-siteprerequisitesatsplicedonor/acceptorareconserved- RemarkabletendencyoflncRNAs tohaveonly2exons(42%,mRNAs:6%)

BUT:LncRNAscontainfewerINTRONs!!mostlncRNAhaveonly1intron!!!;mRNAs3-6

Introns/Exons fromlncRNAsareslightlylonger

COMPARINGmRNAs- lncRNAs

COMPARINGmRNAs- lncRNAs

- lncRNAs areonaveragemuchshorter:ca.500nt- mRNAsarelongerandhavewidersizedistribution

- lncRNAs areuniformà littlealternativesplicing- mRNAs:largevarietyofalternativesplicing

COMPARINGmRNAs- lncRNAs

conservation conservation conservation

EXONS:mRNA:highconservationlncRNA:reducedconservationBut: conservationishigherthanmRNAintron conservation

INTRONS:mRNA:higherconservationthanlncRNAs

EvolutionalconservationoflncRNAs

BLASTofhumanlncRNAs against all availablemammalian genomes andidentify homologousgenes inother species:30%oflncRNA transcripts (n =4546)appear tobeprimatespecific.

Atotal of0.7% (101)oftranscriptsappear tobespecific tothehumanlineage.Asimilar number (134;1.0%)is foundinall ofthe18species analyzed here.

lncRNA

transcrip

ts

species

MostlncRNAtranscriptsareconservedin4-6species

lncRNAs showrelevantspeciesspecificity

COMPARINGmRNAs- lncRNAsChromatinsignaturesattranscriptionalstartsitesareconservedbetweenmRNAsAndlncRNAs:MOSTlncRNAsARETRANSCRIBEDBYRNAPol II

Notshown:RNAPolIIpeaksattranscriptionstartsiteofmostlncRNAs

mRNAlncRNA 5psupportlncRNA

COMPARINGmRNAs- lncRNAs

AbsoluteexpressionoflncRNAsismuchlowerthanmRNAexpression

RNA-seq

COMPARINGmRNAs- lncRNAs

Microarry

AbsoluteexpressionoflncRNAsismuchlowerthanmRNAexpression

COMPARINGmRNAs- lncRNAs

mRNAsshowbroadexpressionindifferenttissues–65%ofmRNAsareexpressedin16tissues

lncRNAs showtissue/cellsoecifcexpression–50%oflncRNAsexpressedin4-5tissues.

lncRNAs locatemorefrequentlytochromatinthanmRNAs

lncRNAs locatemorefrequentlytothenucleusthanmRNAs

DeterminationoftranscriptabundanceNucleus/cytoplasma

DeterminationoftranscriptabundanceChromatin/nucleus

Data:RNAseq ofRNAslocatedinthenucleoplasmaandstickingtochromatin

Data:RNAseqofRNAslocatedinthenucleoplasmaandcytoplasma

COMPARINGmRNAs- lncRNAs

COMPARINGmRNAs- lncRNAs

lncRNAexonsHavearemarkablePotentialtoencodefunctionalsmallRNAs(sRNAs)HIGHERTHANEXONSOFmRNAS!!!!snoRNA:Small nucleolar RNAs (snoRNAs) areaclassofsmall RNAmolecules thatprimarilyguide chemical modifications ofother RNAs,mainlyribosomal RNAs, transfer RNAs andsmallnuclear RNAs.snRNA: Smallnuclear ribonucleic acid(snRNA), alsocommonly referred toasU-RNA, isaclassofsmall RNAmolecules thatarefound within the splicing specklesandCajal bodies ofthecell nucleus ineukaryoticcells.tRNA: translationmiscRNAs: MiscRNA isshort formiscellaneous RNA, ageneral term foraseries ofmiscellaneous smallRNA.Itservesavarietyoffunctions, including some enzyme-likecatalysis andprocessing RNA after it isformed. Besides, some ofthesesmall RNAsmayserveasswitches.

COMPARINGmRNAs- lncRNAs

lncRNAsrepresentabigclassoffunctionalelementsthat- controlledgeneexpression- areprocessed- lackproteincodingpotential- definedlocalization- frequentlyencodesRNAs- lowoverallconservation- 35%oflncRNAsareprimatespecific- expressionisratherlow– butcontrolled!- mostlytranscribedbyRNAPolII

FUNCTION:FORTHEVASTMAJORITYOFlncRNAsTHEBIOLOGICALFUNCTIONISUNKNOWN!!!!