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RNA nucleoprotein complexes in biological systems

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Proceedings of the Indian National Science Academy Aims and scope Submit manuscript

Abstract

RNA-nucleoprotein (RNP) complexes are pivotal to the regulation of gene expression. These multiprotein, multifunctional complexes act as scaffolds, as molecular platforms, as hubs of interaction between the RNA and the proteins. The past decade has seen an exponential increase in the methodologies to identify and functionally characterize these complexes. In this review, we provide an overview of the recent advances in methodologies and the knowledge gained by characterizing these important complexes. This information has provided clues to the role of sequence, and structural determinants for RNA–Protein interaction networks in physiology and pathophysiology. With the recent studies implicating the role of RNA in the formation of biomolecular condensates, their role in health and disease warrants detailed sequence, structure and functional investigations.

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Abbreviations

AD:

Alzheimers disease

AD:

Autosomal dominant

ADHD:

Attention deficit hyperactive disorder

ADPD:

Attention deficit passive disorder.

ALS:

Amyotrophic lateral sclerosis

AR:

Autosomal recessive

ALKBH5:

AlkB homolog 5 RNA demethylase

APEX-Seq:

APEX-2 mediated cross-linking and sequencing

APP:

Amyloid precursor protein

ARM:

Arginine rich motif

ASD:

Autism spectrum disorder

ATXN2:

Ataxin 2 protein

BD:

Bipolar disorder

CARIC:

Click chemistry assisted RNA-interactome capture

CCR4/NOT:

Carbon-catabolite repression 4-negative on TATA-less

CHART-MS:

Capture hybridization analysis of RNA targets

ChIRP-MS:

Comprehensive identification of RNA-binding proteins by mass spectroscopy

CLIP:

Cross-linking and immunoprecipitation

CRAC:

Cross-linking and cDNA analysis

CRUIS:

CRISPR based RNA based interacting system

DCP1/DCP2:

Decapping protein 1 and 2

DSRM:

Double stranded RNA binding motif

eCLIP:

Enhanced CLIP

ED:

Edmann degradation

FCS:

Fluorescence correlation spectroscopy

FISH:

Fluorescence in-situ hybridization

FMRP:

Fragile X mental retardation protein

FRAP:

Fluorescence recovery after photobleaching

FRET:

Fluorescence resonance energy transfer

FUS:

Fused in sarcoma

FTD:

Frontotemporal dementia

FTO:

Fat mass and obesity-associated

HD:

Huntington’s disease

HTT:

Huntington’s disease gene huntingtin

hnRNP:

Heterogeneous nuclear ribonucleoprotein.

HTR-SELEX:

High-throughput systematic evolution of ligands by exponential enrichment.

IP:

Immunoprecipitation.

KH Motif:

K-Homology motif

m6A:

6-Methyl adenosine

MATR3:

Matrin 3

MD:

Mood disorder

MDD:

Major depressive disorder

METTL3/14:

Methyltransferase like protein 3/14

MLO:

Membraneless organelles

MS:

Mass spectrometry

Mu:

Multifactorial

NMIA:

N-Methylisatoic anhydride

NMR:

Nuclear magnetic resonance spectroscopy

OMIM:

Online Mendalian Inheritancein Man

PAN2/PAN3:

Poly(A) nuclease deadenylation complex

PAZ:

Piwi/Argonaute/Zwille

PABP:

Poly(A) binding protein

PAR-CLIP:

Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation

PD:

Parkinsons disease

PIWI:

P-element induced wimpy testis

QKI:

Quackinguiable protein 1

RaPID:

RNA–protein interaction detection

RAP-MS:

RNA antisense purification coupled with mass spectrometry

RNP:

Ribonucleoprotein

RNA:

Ribonucleic acid

RBP:

RNA binding protein

RRM:

RNA recognition motif

RGG:

Arginine glycine glycine motif

RNP-CSI:

RNP consensus sequence

RBD:

RNA binding domain

RBM-45:

RNA binding motif 45

SCA2:

Spinocerebellar ataxia 2

SCZ:

Schizophrenia

SG:

Stress granules

SHAPE:

Selective 2′-hydroxyl acylation and primer extension

SF:

Splicing factor

SMN:

Spinal muscular atrophy

snRNP:

Small nuclear ribonucleoprotein

TARDBP/TDP-43:

Transactive response DNA binding protein

TDP-43:

TAR DNA binding protein

TRAP:

Translating ribosome affinity purification

TRAPP:

Total RNA associated protein purification

TRIBE:

Targets of RNA-binding proteins identified by editing

UPS:

Ubiquitin proteosome system

XLD:

X linked dominan

XNR1:

Xenopus nodal related-1

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Acknowledgements

Work in the authors’ laboratory is supported by research funding from Indian Institute of Science Education and Research Berhampur, Department of Science and Technology-SERB. PM is a KVPY fellow. RSB is a DBT Ramalingaswami Fellow. The authors have made the best efforts to cite as many original citations and review articles as possible. However, due to the vast scope of the review topic, there may be some references which may not have been cited.

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  1. Pratyush Mishra and S. H. Harsha Sankar have contributed equally to this work.

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  1. RNP Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Transit Campus, Govt ITI Building, Engineering School Junction, NH 59, Ganjam, Berhampur, Odisha, 760010, India

    Pratyush Mishra, S. H. Harsha Sankar, Nishad Gosavi & Ruthrotha Selvi Bharathavikru

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Mishra, P., Sankar, S.H.H., Gosavi, N. et al. RNA nucleoprotein complexes in biological systems. Proc.Indian Natl. Sci. Acad. 88, 300–323 (2022). https://doi.org/10.1007/s43538-022-00087-0

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