Non-Coding RNA and Riboregulation

What are ribozymes?

RNA molecules that act as enzymes

What functions do non-coding RNAs perform?

RNA processing, chromosome end-maintenance, viral defense, gene dosage compensation, protein sorting, regulation of development and gene expression

Who discovered ribozymes?

Altman and Czech

What is the RNA world hypothesis?

RNA is the primordial molecule that life on earth evolved from, RNA preceded DNA and proteins

What is RNP?

RNA + protein molecule complex

What percent of total transcripts are ncRNAs?

98%

What are some house-keeping ncRNAs?

rRNA, tRNA, snRNA, snoRNA, RNase P, SRP, telomerase guide

What are the types of regulatory ncRNAs?

short, long, prokaryoticW

What are the short, regulatory ncRNAs?

miRNA, siRNA, piRNA

What are some long, regulatory RNA?

XIST, H19, HOTAIR

What are some prokaryotic, regulatory RNA?

sRNAs, CRISPR, antitoxin, riboswitch

What is RNA-mediated gene silencing?

system that responds to double-stranded RNA to selectively trigger silencing of gene expression

What are the RNAs involved in RNA-mediated gene silencing?

siRNA, miRNA, piRNA

What are piRNAs?

mainly expressed in germ cells, protect the germline genome from active retrotransposons

What are the related gene silencing phenomena in RNA-mediated gene silencing?

RNAi (PTGS), co-suppression, transcriptional gene silencing (TGS), miRNAs

What is RNAi?

dsRNA selectively and potently silence target gene expression by a mechanism that leads to degradation of the target mRNA

What is co-suppression?

expression of a transgene suppresses expression of the corresponding endogenous gene

What is the first type of TGS?

dsRNA-dependent DNA methylation of promoter regions turns off gene transcription, dsRNA regulates heterochromatin formation, RNA-mediated methylation of histone proteins

What is the second type of TGS?

in ciliates, dsRNA influences developmental-regulated, DNA rearrangement and elimination

What are dsRNA transcripts that trigger TGS generated by?

divergent transcription

What are miRNAs?

short RNAs (22nt) that specifically interact with particular mRNAs (3’ UTR) to degrade or prevent translation of specific genes

What will miRNA degrade?

perfect complementary between miRNA and target RNA

What will miRNA prevent translation?

imperfect complementary between miRNA and target RNA

Where was the first miRNA discovered?

in worms

How are miRNAs synthesized?

as longer precursor RNAs that become processes to dsRNA precursors that are processed to single-stranded effector RNAs interact with specific mRNA sequences to shut down target gene expression

What synthesizes the longer precursors RNAs that lead to miRNA?

Drosha, RNAase III ribonuclease

What processes single-stranded effector RNAs that lead to miRNA?

Dicer, RNAse III ribonuclease

What are piRNA derived from?

transcription of specific gene clusters and from active transposon mRNA

What are single-stranded piRNAs processes by?

a largely unknown but Dicer-independent mechanism

What is the initiation step of RNAi?

dsRNA is recognized by machinery (DICER) that converts it into siRNAs

What is the structure of siRNA?

5’ phosphate and 2 nucleotide overhangs at 3’ end

What is the structure of DICER?

catalytic domain, dsRNA binding domain, helicase domain, PAZ domain

What is the effector step of RNAi?

siRNA are recognized by RISC forming an RNP that contain ribonuclease activity

What does RISC stand for?

RNA-induced silencing complex

What does the RISC complex contain?

an effector nuclease SLICER responsible for destroying target RNA

What is SLICER a member of?

the argonaute family of proteins

What is the first amplification step of RNAi?

dsRNA is converted into many siRNAs and each siRNA can potentially target a different region of a specific mRNA

What is the second amplification step of RNAi?

catalytic mechanism, each siRNA acts multiple times

What is the third amplification step of RNAi?

RNA-dependent RNA polymerases exist in some organism capable of amplifying target RNAs to generate secondary siRNAs

What are the biological roles of RNAi?

immune system of genome, silencing of endogenous genesW

What are the applications of RNAi?

probing gene function, combat viral infection, treat genetic diseases

Why can RNAi be used as a genetic tool?

offers the ability to specifically inactivate particular target genes so that the functional loss of gene product can be examined

How can RNAi be used as the immune system of the genome?

antiviral defense, suppress transposon activity

What percent of the human genome consists of remnants of previous virus/transposon invasions?

45%

What is the estimated number of miRNA genes in humans?

>2000

How many mRNAs can each miRNA target?

10-100s

What are lncRNAs?

long non-coding RNA with no protein coding potential

What roles do lncRNAs play?

gene expression using diverse molecular mechanisms (signals, decoys, guides, scaffolds)

What are lncRNAs linked to?

a broad range of human diseases

What are some lncRNAs?

XIST, HOTAIR, LincRNA-p21, NEAT1, MALAT

What are XIST and TSIX involved in?

X chromosome inactivation and gene dosage compensation

What is HOTAIR involved in?

repression of Hox genes which regulate development

What are the functions of lncRNAs?

RNA decoys, miRNA sponges, RNA or protein binding and acting as scaffolds, recruitment of chromatin modifying complexes to their DNA targets, post-transcriptional regulation

What is the RNA decoy function of lncRNA?

titrating transcription factors away from their DNA targets by binding to them as target mimics

What is the miRNA sponge function of lncRNAs?

certain miRNAs work at the post-transcriptional level as miRNA targe site decoys, titrating miRNA effector complexes away from their mRNA targets

What is the RNA or protein binding and acting as scaffold function of lncRNAs?

many lncRNAs binds to specific combinations of regulatory proteins, acting as scaffold elements within ribonucleoprotein complexes

What is the recruitment of chromatin-modifying complexes to their DNA targets function of lncRNAs?

happens in cis or trans

What is the post-transcriptional regulation function of lncRNAs?

modulate direct processing of their mRNA targets, including translation, splicing, and degradation