Non-coding regulatory RNAs

Non-coding RNAs

functional RNA molecules that are trascribed from DNA, but not translated into protein

• only 1-3% of the genome is translated into protein (ex. mRNA)

• the rest of the transcriptome is made up of non-coding RNAs

Types of non-coding RNAs

classified on function and size

housekeeping ncRNAs:

• sometimes called structural ncRNAs or functional ncRNAs tend to plau functional roles in cellular processes (translation and splicing)

Regulatory ncRNAs:

• regukate cellular processes (transcription, gene expression, splicing, translation)

• broken into 2 categories based on size

  • small ncRNA (<200 nt)

  • long ncRNA(>200 nt)

Housekeeping small non-coding RNAs: rRNA

Ribosomal RNAs (rRNAs): interact with ribosomal proteins to make the ribosome which is critical for protein translation

• majority of RNA in the cell (80%)

Biosynthesis:

• transcribed in nucleolus from rDNA genes found in tandem repeats throughout the genome

• modified and folded into structural RNAs that can interact with other RNAs and proteins

Housekeeping small RNAs: tRNAs

adapters that link the mRNA and the amino acid during protein synthesis (translation)

• each tRNA binds a single amino acid via the acceptor stem (amino acid binding arm) and brings it to the ribosome

• anticodon arn has 3 bases that are complementary to a codon mRNA

biosythesis

• encoded by specific genes scattered throughout the genome

• transcribed as pre-tRNAs from their own highly conserved promoters

• pre-tRNAs are spliced and processed in the nucleus and then fold into a secondary structure

Housekeeping small non-coding RNAs: snRNAs

Small Nuclear RNAs: structural RNAs that are a major component of the spliceosome

• the spliceosome is a large, protein-RNA complex that consists of 5 snRNAs (U1 to U6) and over 150 proteins

• aid in the regulation of transcription factors and maintenance of telomeres

biosynthesis:

• introns of mRNAs and liberated by splicing or transcribed from their own promoters (BOTH)

Housekeeping small non-coding RNAs: snoRNAs

small nucleolar RNAs: primarily “guide” chemical modificatons (methylations and pseudouridylation) of the other RNAs (rRNAs, tRNAs, and snRNAs)

• complexes with proteins to form a complex referred to as a small nucleolar ribonucleoprotein partical (snoRNP)

• acts as a guide that binds target RNA through complementary base-pairing

Biosynthesis

• as intronts of mRNAs and liberated by splicing or transcribed from their own promoters (BOTH)

Housekeeping small non-coding RNAs: scaRNAs

a class of snoRNAs that localize to the Cajal body

• primarily responsible for the modifications of other RNAs

• some scaRNAs are precursers to other ncRNAs

Biosynthesis

• most as introns of mRNAs liberated by splicing, but sime have their own promoters (BOTH KINDA)

regulatory small ncRNAs: PIWI-interacting RNAs (piRNAs)

silence transposable elements to maintain genomic instability (2 mechanisms)

• no secondary structure (completely linear)

• pi biogenesis mainly occurs in the germline and some somatic cells (stem cells and neurons)

Biosynthesis

• synthesized as precursor piRNAs from piRNA clusters, active transposable elements, or in UTRs of other RNAs (BOTH)

• piRNA precursor is cut into piRNA intermediates which are then loaded into Piwi proteins and modified to yeild primary piRNA

• a secondary biogenesis pathway exists called ping pong amplification: creates a lot more of the piRNAs

regulatory small ncRNAs: MiRNAs/ siRNAs

MicroRNAs/ small interfering RNAs: regulate gene expression by binding to mRNAs and IncRNAs and either blocking translation or promoting RNA decay

siRNAs use complementary base pairing to recruit RISC to target mRNAs

• if base pairing is perfect → mRNA degradation

• if imperfect → suppression of translation of mRNA

one miRNA can target many genes bc can be an imperfect fit

miRNA biogeneisis

• in canonical pathway, miRNA genes are transcribed from their own promotor, then are modified (capping and poly-A) and folded into hairpin structure-primary miRNA

• Pri-miRNA is cleaved by Drosha and DGCR8 into pre-miRNA and then exported from the nucleus

• in a non-conical pathway, gene is an intron of mRNA (called mirtron) is spliced out to form the pre-miRNA

• in cytoplasm pre-mRNA is processed by Dicer into a miRNA duplex then unwound by Argonaut

• one strand is loaded into RISC complex

• now called a small infering RNA (siRNA)

Transposable elements (TE) and classes

repetative DNA fragments that can “jump” around the genome

• if they land in or near other genes, they can mutate or alter the transcription of that gene → genomic instability

Two main types:

• class 1 (retrotransposon): use “copy and paste” - transcribed into RNA → reverse transcribed into DNA → inserted into a new location

  • sometimes called virus-like transposon

• class 2 (DNA transposon): Use “cut and paste” - transposon enzyme cuts out TE and pastes it into new location

transposons contain genes that encode the reverse transcriptase (class 1) or transposase (class 2) necessary for copy and paste or cut and paste

LncRNAs

Long non-coding RNAs: long RNAs (>200 nt) with no obvious open reading frame (ORF)

• classified based on where they are made from within the genome

function:

• functions both in the nucleus and the cytoplasm. can influence chromosome architecture, transcription, translation, epigenetic regulation, protein localization, and protein function

Biosynthesis

• encoded by genes that typically have their own promoters

• promoters are simular to protein-coding genes so IncRNAs are expressed in a developmental, cell type-specific, and context-dependent manner

• processed like mRNAs

• can be alternatively spliced like mRNAs

• some evidence that they get translated into proteins

CircRNAs

• single stranded RNA that is a closed structure because 5’ and 3’ ends covalently linked

• generated by post transcriptional processing of mRNAs or IncRNAs

• lack of exposed 3’ or 5’ nucleotides so are resistant to nuclease activity and very stable

Biosynthesis

• generated by non-canonical splicing of mRNA and IncRNA (called backsplicing)