RNA and gene regulation

Organellar ribosomal RNA

Organellar ribosomal RNA is the rRNA inside mitochondrial and chloroplast ribosomes, ranging from bacterial-like forms in plants and chloroplasts to drastically shortened ones in animals.

Origin of the spliceosome

The origin of the spliceosome is traced to group II introns, self-splicing mobile ribozymes that invaded eukaryotic genes at the origin of eukaryotes, likely via mitochondria.

Orphan nuclear receptors (ONRs) are nuclear receptor transcription factors identified without known endogenous ligands; 24 of 48 human NRs were once orphans, with ligands such as lipids, heme, and phospholipids since found for ROR, REV-ERB, and others.

Oskar (gene)

oskar (osk) is a Drosophila maternal-effect gene, necessary and sufficient for germ plasm assembly; its mRNA localizes to the oocyte posterior via kinesin, directs nanos localization, and encodes Long and Short Oskar isoforms.

OTX2

OTX2 (orthodenticle homeobox 2), also MCOPS5/CPHD6, is a homeobox transcription factor gene on chromosome 14q22.3 essential for forebrain, eye, and pituitary development; mutations cause microphthalmia and pituitary deficiency.

P-TEFb

P-TEFb (positive transcription elongation factor b) is the CDK9–cyclin T complex that releases paused RNA polymerase II into productive elongation; regulated by 7SK snRNP/HEXIM1, central to HIV Tat transactivation and a cancer drug target.

P14arf

p14ARF (p19Arf in mouse) is a 132-amino-acid tumor suppressor encoded by CDKN2A on 9p21 from an alternative reading frame; it stabilizes p53 by sequestering MDM2 in the nucleolus and is frequently lost or methylated in cancer.

P300-CBP coactivator family

p300-CBP coactivator family (p300/CBP, KAT3): histone acetyltransferase coactivators CBP (CREBBP), p300 (EP300), and PCAF; bridge transcription factors to basal machinery, acetylate H3K18/K27, essential in mice, mutated in Rubinstein-Taybi syndrome and cancer.

p53 tumour suppressor family

p53 tumour suppressor family: transcription factors p53, p63, and p73 (TP53/TP63/TP73). p63 and p73 are ancestral homologs acting in development; p53, mutated in ~50% of cancers, guards the genome.

Palindromic sequence

Palindromic sequence: a DNA or RNA motif identical to its reverse complement, read 5'-to-3' on both strands; basis of restriction enzyme sites (EcoRI GAATTC), hairpin/cruciform structures, genome instability, and the CRISPR name.

PAN2-PAN3 deadenylation complex catalytic subunit PAN2

PAN2 (USP52, DEDCRF) is the catalytic DEDD-family 3'-to-5' exoribonuclease subunit of the PAN2-PAN3 deadenylation complex, which with Ccr4-Not performs biphasic cytoplasmic poly(A) tail shortening, trimming distal tails in the initial slow phase.

Panoramix

Panoramix (Panx, CG9754, Silencio) is a Drosophila melanogaster nuclear protein essential for piRNA-guided transcriptional silencing of transposons, acting downstream of Piwi in the SFiNX complex and required for fertility.

Sep 29, 2026

PAR-CLIP

PAR-CLIP is a molecular biology method that maps RNA-binding protein binding sites across the transcriptome at single-nucleotide resolution, introduced by Markus Hafner and colleagues in 2010.

Sep 29, 2026

Parallel analysis of RNA structure (PARS)

Parallel analysis of RNA structure (PARS) is a high-throughput sequencing method measuring RNA secondary structure transcriptome-wide, introduced by Michael Kertesz and colleagues in Nature in 2010.

PAX5

PAX5 (paired box 5, BSAP) is a paired-domain transcription factor essential for B cell lineage commitment and identity; it activates B-lineage genes, represses others, and is frequently altered in B-ALL and lymphoma.

PDX1

PDX1 (IPF1, IDX-1, STF-1) is a homeodomain transcription factor, master regulator of pancreas development and beta-cell identity; homozygous mutation causes pancreatic agenesis, heterozygous mutation causes MODY4 diabetes.

Peptidase S48, DNA-binding transcriptional activator HetR

HetR, classified in protein databases as the serine protease Peptidase S48, is a 299-amino-acid DNA-binding transcriptional activator of filamentous cyanobacteria that acts as master regulator of heterocyst differentiation, identified in Anabaena sp. PCC 7120 in 1991.

Peptide chain elongation

Peptide chain elongation: the translation stage in which ribosomes decode mRNA codons, form peptide bonds, and translocate, using eEF1A, eEF2, and eIF5A at 3–5 amino acids per second; a major antibiotic target.

Peptide chain release factor

Peptide chain release factors (RF1, RF2, RF3 in bacteria; eRF1, eRF3 in eukaryotes) are proteins that recognize stop codons and hydrolyze peptidyl-tRNA to terminate translation, with unrelated bacterial and archaeo-eukaryotic lineages.

Perinucleolar compartment

Perinucleolar compartment (PNC): a membraneless cancer-cell nuclear body at the nucleolar periphery, 0.25–4 µm, enriched in pol III noncoding RNAs and RNA-binding proteins like PTB, correlating with metastasis.

Peroxisome proliferator-activated receptor

Peroxisome proliferator-activated receptors (PPARs): PPARα, PPARβ/δ, PPARγ, ligand-activated nuclear receptors cloned by Issemann and Green in 1990, heterodimerizing with RXR to regulate lipid and glucose metabolism; targets of fibrates and thiazolidinediones.

Peroxisome proliferator-activated receptor alpha

Peroxisome proliferator-activated receptor alpha (PPARα, NR1C1, PPARA) is a fatty acid-sensing nuclear receptor regulating lipid catabolism; target of fibrates, with PROMINENT trial failure and rodent-specific peroxisome proliferation.

Peroxisome proliferator-activated receptor gamma

PPARγ (PPARG, NR1C3) is a nuclear receptor and master regulator of adipocyte differentiation and insulin sensitivity; thiazolidinedione diabetes drugs target it, and dominant-negative PPARG mutations cause FPLD3 lipodystrophy.

PGC-1

PGC-1 (PPAR gamma coactivator-1) family of transcriptional coactivators: PGC-1α, PGC-1β, and PRC, master regulators of mitochondrial biogenesis and energy metabolism, cold- and exercise-inducible, linked to diabetes, heart failure, and neurodegeneration.

PGC-1 and ERR-induced regulator in muscle protein 1

PGC-1 and ERR-induced regulator in muscle protein 1, encoded by the PERM1 gene, is a transcriptional regulator of mitochondrial metabolism expressed mainly in skeletal and cardiac muscle.

Phenylalanyl-tRNA synthetase

Phenylalanyl-tRNA synthetase (PheRS), EC 6.1.1.20, a class II aminoacyl-tRNA synthetase charging tRNA^Phe with phenylalanine; exists as bacterial and cytosolic (αβ)2 heterotetramers and a monomeric mitochondrial form; edits mischarged Tyr-tRNA^Phe in its β-subunit B3/B4 domain.

Phosphonate utilization transcriptional regulator PhnR

PhnR (phosphonate utilization transcriptional regulator) is a bacterial regulator of phosphonate uptake and catabolism genes; LysR-like in Pseudomonas fluorescens 23F (phosphonoacetate induction, biosensors), GntR-family repressor in P. putida KT2440.