Transcription and RNA II Flashcards
RNA in the cell
always found in the cell associated with proteins as ribonucleotideprotein complex; proteins are required for RNA to function (RNA cap Pol A binding proteins) and are protect RNA from degradation
Large ribonucelotideprotein complexes
can act as molecular machines to perform repetitive tasks such as RNA splicing and protein synth
mRNA
messenger RNA, codes for proteins
rRNA
ribosomal RNA form basic structure of ribosome and catalyze protein synth
tRNA
transfer RNA central to protein synth as adaptors between mRNA and amino acids
snRNA
small nuclear RNA; function in a variety of nuclear functions including splicing of pre-mRNA
snoRNA
small nucleolar RNA; help to process and chemically modify rRNAs
miRNA
microRNAs regulate gene expression by blocking translation of specific mRNA and cause their degredation (inhibit expression of specific mRNAs); 1st identified in nematode C.elegans; double stranded
siRNA
small interfering RNA; turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structures; first identified in plants; response triggered by dsRNA (double stranded); use for gene silencing and knockdown; double stranded
piRNA
piwi-interacting RNAs; bind to piwi proteins and protect germ line from transposable elements;
lncRNA
long non-coding RNA; serve as scaffolds, regulate diverse cell population, including X chromosome inactivation
primary transcript of protein coding gene
undergoes premRNA processing in nucleus to make mature mRNA; mRNA directs synthesis of protein once in cytoplasm
types RNA broadly
mRNA and non coding RNA which can be house keeping or regulatory
housekeeping ncRNA
tRNA rRNA
regulatory ncRNA
lncRNA and small ncRNA (microRNA, snoRNA, siRNA, snRNA, and piRNA)
Pre-mRNA processing
RNA capping RNA splicing RNA cleavage and polyadenylation
C-terminal tail of RNA Pol II
many of the processing factors bind to phosphorylated C terminal tail of RNA pol II and travel with the enzyme as RNA is synthesized
RNA capping
7’methyguanisin cap attached to 5’end nascent RNA by 5’ 5’ linkage; cap structure needed for RNA splicing, mRNA transport out of nucleus, mRNA stabilization, and translation of most mRNA
nuclear cap binding complex
mediates role of cap in nucleus
cytoplasmic eucaryotic initiation factor 4E
mediates role of cap in cytoplasm; targeted by viruses and misrelated in many cancers
RNA splicing
introns removed exons spliced together occurs in several steps uses lots ATP
narcolepsy in doberman
caused by splicing deffect insertion of repetitive element (SINE) w in intron 3 of hypocretin receptor2 gene leads to exon 4 not being retained bc 3’ splice site adjacent to exon 4 not recognized bc splice some not positioned correctly so 3’ splice site adjacent to exon 5 used instead
splicesome
large ribonucleoprotein complex that does RNA splicing
cis-splicing
splicing exons in same pre-mRNA molecule (usually this)
trans-splicing
splicing exons of different pre-mRNA molecules (happens under certain conditions)
Requirements for normal splicing
conserved RNA sequence at 5’ splice site, branch sequence, 3’ splice site, polypyrimadine tract located between branch sequence and 3’ splice site
splicing steps
- begins with 2’ hydroxyl of adenine nucleotide in branch sequence attacking upstream intron/exon junction
- New phosphodiester bond formed leading to lariat structure; generating reactive hydroxyl group at 3’ end of exon
- 3’ hydroxyl attacks downstream intron/exon junction
- new phosphodiester bond created btwn 2 exons and releasing intron
alternative splicing
different exons included in final transcript resulting in production of different mRNAs from same gene (90% primary transcripts from spliced genes alternatively spliced)
increasing proteome complexity
spliced mRNA can encode proteins with distinct functional, structural, and regulatory properties
splice variants in tumor
often promote proliferation, survival, and metastasis of cancer cells
exons included in transcript
regulated by protein factors that bind to intronic and exonic sequences in RNA which promote or inhibit activation and assembly of splicsosome at specific site controlling whether exon is included in mature mRNA
final step of pre-mRNA processing
occurs when RNA cleavage and poly A signals encoded in DNA are transcribed and recognized in RNA by proteins which cleave mRNA and add poly A tail
poly A polymerase
post transcriptionally adds poly A tail to 3’ end processed RNA
poly A tail
protects mRNA from degradation, tail shortens with each round of transcription
poly A binding protein
required for mRNA to exit nucleus and to be efficiently translated
stable mRNA
in general capped mRNA with poly a tail protected from degradation until poly A tail shortened as mRNA is translated; stability also regulated by specific nucleotide sequences and structural elements; these mRNA specific features bound to protein complexes that promote or inhibit mRNA degradation
microRNA and small interfering RNA
regulate gene expression by promoting degradation of mRNA containing specific recognition sequence
mRNA half lives
30min-15hrs; those encoding regulatory proteins (if TF) 30min those encoding structural protein (actin) 15hrs
mRNA surveliance
cells assess mRNA quality as it is being translated and those that are abnormal get degraded before translation into protein complete
nonsense mediated decay
mRNAs containing premature stop codons are recognized and degraded
regulation of mRNA translation effect on cell
by regulating mRNA translation cells can rapidly change protein levels and consequently cell behavior in response to changes in internal and external envionrment
4 phases of translation
initiation, elongation, termination, and recycling
rate- limiting for protein synthesis
40S ribosome recruitment to mRNA during intiaiton important bc rate limiting for protein synth and frequently misregulated in disease
circularization of mRNA
critical step required for ribosome recruitment and efficient translation of mRNA, required for initiation; circularization regulated by mTOR
Steps of circularization of mRNA
in cytoplasm cap binding protein eIF4E interacts with eIF4G (initiation factor) once exit nucleus this complex displaces nuclear cap binding complex and binds to 5’ cap of mRNA eIF4G binds to poly a tail binding protein and brings 5’ and 3’ ends together to form circular structure
mTOR
mechanisitic target of rapamycin; master regulator of cell metabolism and growth; this is a protein kinase; coordinates environmental input with cell metabolism and growth; works by controlling eIF4E which is inactive when bound to inhibitory protein 4EBP, mTOR phosphorylates and inactivates 4EBP which allows eIF4E to promote circularization and translation of capped mRNA
mTOR in abundant nutrients
is activated and phosphorylates specific substrates that stimulate synthesis of lipids, nucleotides, proteins needed for cell growth and proliferation
mTOR in nutrient starvation and energy depletion
is inhibited and consequently translation is inhibited
mTOR and cancer
mTOR being activated stimulates cell growth and proliferation and may be hyper activated in cancer cases where mTOR leads to translation of proteins that promote specific tumor cell behaviors such as cell proliferation and survival, angiogenesis, tissue invasion, and metastasis
viruses and cell replication
many viruses use virally encoded proteins to disrupt cell translational machinery and preferentially translate viral proteins
disregulation of ncRNA
associated with neurodegeneration, immune disorders, cancer
lncRNA
long non coding RNA; these have ability to regulate cellular processes via hybridization (base pairing) with specific DNA and RNA sequences; can also fold into 3D structures capable of binding specific proteins
what do lncRNA regulate
nuclear architecture, transcription, post transcriptional processing, mRNA stability, and protein synthesis
interfering RNA (RNAi)
both miRNA and siRNA inhibit gene expression and are considered interfering RNA; can use term RNA interference, gene silencing or gene knockdown; BOTH miRNA and siRNA are double stranded, recognize specific mRNA targets by base pairing
dsRNA
usually siRNA perfect complement to target sequence while miRNA partially complimentary; both inhibit target mRNAs by stimulating degradation or blocking translation
endogenous gene transcripts
miRNA derived from this; miRNA precursors transcribed by RNA pol II, capped, and polyadenylated in the nucleus
miRNA vs siRNA
since miRNA only partially complimentary it has ability to target transcripts of 100s of genes simultaneously
miRNA production
derived from dsRNA precursor; transcribed and processed in nucleus to produce double stranded miRNA precursor (pre-miRNA) which is exported to cytoplasm
dicer
cleaves dsRNA progenitor of siRNA and the pre-miRNA in cytoplasm to produce mature versions
RNA induced silencing complex (RISC)
miRNA and siRNA both associate with an argonuate protein as part of this; one strand of mi or si RNA used to direct RISC to mRNA target; w/ siRNA argonuate cleaves mRNA and promotes its degradation; miRNAs inhibit or promote degradation
what does miRNA regulate
differentiation, proliferation, apoptosis; specific miRNAs for cardiac development, stem cell differentiation and regeneration
altered miRNA
associated with cardiovascular disease, endocrine disorders, and cancer
oncogene miRNA
over expressed in cancer; can act as oncogenes by inhibiting expression of genes that block tumorigenesis (tumor suppressor genes)
tumor supressor miRNAs
inhibit the expression of oncogene mRNAs; often underexpressed or inactive in tumors
RNAi in lab
used to silence genes to see what their function is; SIRT1 which is associated with pancreatic cancer is down regulated by RNAi making cells undergo apoptosis; RNAi against hair growth inhibitor makes long hair mouse; siRNA can be used to perform genome wide screening to ID novel signaling pathways and ID drug targets
RNAi in clinic
being tested for metabolic, cardiovascular disorders, viral diseases and cancer with some success and some failure most recently was used to treat hereditary transthyretin amyloidosis (drug name is onpattro); some success in clinical trails treating cardiovascular disease and hemophilia
Onpattro
FIRST RNAi drug to be FDA approved; lowers expression of mutant transthyretin gene
