Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

TY - JOUR

T1 - Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

AU - Yap, Karen

AU - Lim, Zhao Qin

AU - Khandelia, Piyush

AU - Friedman, Brad

AU - Makeyev, Evgeniy

PY - 2012/6

Y1 - 2012/6

N2 - Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and nonneuronal cells. However, in nonneuronal cells, the splicing of 3'-terminal introns within these genes is repressed by the polypyrimidine tract-binding protein (Ptbp1). This inhibits the export of incompletely spliced mRNAs to the cytoplasm and triggers their nuclear degradation. Clearance of these intron-containing transcripts occurs independently of the nonsense-mediated decay (NMD) pathway but requires components of the nuclear RNA surveillance machinery, including the nuclear pore-associated protein Tpr and the exosome complex. When Ptbp1 expression decreases during neuronal differentiation, the regulated introns are spliced out, thus allowing the accumulation of translation-competent mRNAs in the cytoplasm. We propose that this mechanism counters ectopic and precocious expression of functionally linked neuron-specific genes and ensures their coherent activation in the appropriate developmental context.

AB - Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and nonneuronal cells. However, in nonneuronal cells, the splicing of 3'-terminal introns within these genes is repressed by the polypyrimidine tract-binding protein (Ptbp1). This inhibits the export of incompletely spliced mRNAs to the cytoplasm and triggers their nuclear degradation. Clearance of these intron-containing transcripts occurs independently of the nonsense-mediated decay (NMD) pathway but requires components of the nuclear RNA surveillance machinery, including the nuclear pore-associated protein Tpr and the exosome complex. When Ptbp1 expression decreases during neuronal differentiation, the regulated introns are spliced out, thus allowing the accumulation of translation-competent mRNAs in the cytoplasm. We propose that this mechanism counters ectopic and precocious expression of functionally linked neuron-specific genes and ensures their coherent activation in the appropriate developmental context.

KW - coordinated gene expression

KW - neuronal differentiation

KW - presynaptic proteins

KW - polypyrimidine tract-binding protein

KW - intron retention

KW - nuclear mRNA surveillance

KW - NUCLEAR RETENTION

KW - HUMAN TRANSCRIPTOME

KW - SPLICING REGULATION

KW - MAMMALIAN-CELLS

KW - FISSION YEAST

KW - PROTEIN

KW - PTB

KW - DEGRADATION

KW - EXPRESSION

KW - NONSENSE

U2 - 10.1101/gad.188037.112

DO - 10.1101/gad.188037.112

M3 - Article

SN - 0890-9369

VL - 26

SP - 1209

EP - 1223

JO - Genes and Development

JF - Genes and Development

IS - 11

ER -