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Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways

ADAR1 is an adenosine deaminase that converts adenosine to inosine (A-to-I) mostly on Alu repeats in human RNA. Here by analysing transcriptome-wide ADAR1–RNA interactions, the authors show that ADAR1 also binds non-Alusequences to regulate alternative 3′ UTR usage and miRNA biogenesis in the nucleus.

Jae Hoon Bahn
Jaegyoon Ahn
Xinshu Xiao
Research09 Mar 2015
Nature Communications

Volume: 6, P: 1-13
Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans

Cryptococcus neoformans is the leading cause of death by fungal meningoencephalitis. Here, the authors study the roles played by 129 putative kinases in the growth and virulence of C. neoformans, identifying potential targets for development of anticryptococcal drugs.

Kyung-Tae Lee
Yee-Seul So
Yong-Sun Bahn
ResearchOpen Access28 Sept 2016
Nature Communications

Volume: 7, P: 1-16
Genetic variants affecting RNA stability influence complex traits and disease risk

RNAtracker is a computational pipeline that distinguishes variants associated with allele-specific RNA stability from those associated with allele-specific RNA transcription. Variants affecting RNA stability are enriched in immune-related genes and contribute to disease risk.

Elaine Huang
Ting Fu
Xinshu Xiao
Research05 Sept 2025
Nature Genetics

Volume: 57, P: 2578-2588
Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes

The function of rare non-coding variants remains challenging to decipher. Here, the authors developed MapUTR to uncover 10,524 functional rare 3’ UTR variants regulating mRNA abundance, many of which reside in cancer driver genes.

Ting Fu
Kofi Amoah
Xinshu Xiao
ResearchOpen Access18 Apr 2024
Nature Communications

Volume: 15, P: 1-20
Human glutamate dehydrogenase is immunologically distinct from other mammalian orthologues

Sang Ho Jang
A Yeon Kim
Soo Young Choi
ResearchOpen Access01 Aug 2003
Experimental & Molecular Medicine

Volume: 35, P: 249-256
Widespread RNA editing dysregulation in brains from autistic individuals

An overall downregulation of RNA editing was observed in postmortem brains from people with autism, which was consistent across brain regions and genetic disorder subtypes. These changes were regulated by the RNA-binding proteins FMRP and FXR1P.

Stephen S. Tran
Hyun-Ik Jun
Xinshu Xiao
Research17 Dec 2018
Nature Neuroscience

Volume: 22, P: 25-36
Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

Differential binding of RNA-binding proteins mediated by genetic variants (GVs) can influence posttranscriptional regulation. Here, the authors develop BEAPR, a computational approach to identify allele-specific binding events in eCLIP-Seq data.

Ei-Wen Yang
Jae Hoon Bahn
Xinshu Xiao
ResearchOpen Access22 Mar 2019
Nature Communications

Volume: 10, P: 1-15
Hepatocyte-specific Prominin-1 protects against liver injury-induced fibrosis by stabilizing SMAD7

Hyun Lee
Dong-Min Yu
Young-Gyu Ko
ResearchOpen Access29 Aug 2022
Experimental & Molecular Medicine

Volume: 54, P: 1277-1289
Kinetics of mRNA nuclear export regulate innate immune response gene expression

The UCLA Ribonomics group reports that the nuclear export efficiency of innate immune mRNAs varies over a hundred-fold range such that for many genes only a small fraction of the newly synthesized premRNA reaches the cytoplasm. They show that nuclear export and cytoplasmic decay rates are correlated thereby ensuring similar expression levels of short-lived and long-lived mRNAs.

Diane Lefaudeux
Supriya Sen
Sri Kosuri
ResearchOpen Access23 Nov 2022
Nature Communications

Volume: 13, P: 1-16
Regulation of RNA editing by RNA-binding proteins in human cells

Giovanni Quinones-Valdez et al. examined the role of over 200 RNA-binding proteins in mediating A-to-I RNA editing. They identified several RNA-binding proteins that regulate ADAR1 expression, interaction, or binding with Alu elements in a cell type-specific manner.

Giovanni Quinones-Valdez
Stephen S. Tran
Xinshu Xiao
ResearchOpen Access14 Jan 2019
Communications Biology

Volume: 2, P: 1-14
The transgenerational inheritance of autism-like phenotypes in mice exposed to valproic acid during pregnancy

Chang Soon Choi
Edson Luck Gonzales
Chan Young Shin
ResearchOpen Access07 Nov 2016
Scientific Reports

Volume: 6, P: 1-11

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Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways

Systematic functional analysis of kinases in the fungal pathogen Cryptococcus neoformans

Genetic variants affecting RNA stability influence complex traits and disease risk

Massively parallel screen uncovers many rare 3′ UTR variants regulating mRNA abundance of cancer driver genes

Human glutamate dehydrogenase is immunologically distinct from other mammalian orthologues

Widespread RNA editing dysregulation in brains from autistic individuals

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

Hepatocyte-specific Prominin-1 protects against liver injury-induced fibrosis by stabilizing SMAD7

Kinetics of mRNA nuclear export regulate innate immune response gene expression

Regulation of RNA editing by RNA-binding proteins in human cells

The transgenerational inheritance of autism-like phenotypes in mice exposed to valproic acid during pregnancy

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