Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System.

Fernando J Martinez, Gabriel A Pratt, Eric L Van Nostrand, Ranjan Batra, Stephanie C Huelga, Katannya Kapeli, Peter Freese, Seung J Chun, Karen Ling, Chelsea Gelboin-Burkhart, Layla Fijany, Harrison C Wang, Julia K Nussbacher, Sara M Broski, Hong Joo Kim, Rea Lardelli, Balaji Sundararaman, John P Donohue, Ashkan Javaherian, Jens Lykke-Andersen, Steven Finkbeiner, C Frank Bennett, Manuel Ares, Christopher B Burge, J Paul Taylor, Frank Rigo, Gene W Yeo

Neuron · 2016 · Vol. 92 (4) · pp. 780-795

PubMed DOI PMC Full Text

Abstract

HnRNPA2B1 encodes an RNA binding protein associated with neurodegeneration. However, its function in the nervous system is unclear. Transcriptome-wide crosslinking and immunoprecipitation in mouse spinal cord discover UAGG motifs enriched within ∼2,500 hnRNP A2/B1 binding sites and an unexpected role for hnRNP A2/B1 in alternative polyadenylation. HnRNP A2/B1 loss results in alternative splicing (AS), including skipping of an exon in amyotrophic lateral sclerosis (ALS)-associated D-amino acid oxidase (DAO) that reduces D-serine metabolism. ALS-associated hnRNP A2/B1 D290V mutant patient fibroblasts and motor neurons differentiated from induced pluripotent stem cells (iPSC-MNs) demonstrate abnormal splicing changes, likely due to increased nuclear-insoluble hnRNP A2/B1. Mutant iPSC-MNs display decreased survival in long-term culture and exhibit hnRNP A2/B1 localization to cytoplasmic granules as well as exacerbated changes in gene expression and splicing upon cellular stress. Our findings provide a cellular resource and reveal RNA networks relevant to neurodegeneration, regulated by normal and mutant hnRNP A2/B1. VIDEO ABSTRACT.

Publication Types

["Journal Article", "Video-Audio Media"]

Keywords

[]

MeSH Terms

["Alternative Splicing", "Amyotrophic Lateral Sclerosis", "Animals", "Case-Control Studies", "Cell Survival", "D-Amino-Acid Oxidase", "Fibroblasts", "Fluorescent Antibody Technique", "Gene Expression", "Gene Expression Profiling", "Heterogeneous-Nuclear Ribonucleoprotein Group A-B", "Humans", "Induced Pluripotent Stem Cells", "Mice", "Motor Neurons", "Mutation", "Polyadenylation", "Protein Transport"]

Funding

R01 HG004659 NHGRI NIH HHS (United States)

R35 GM118069 NIGMS NIH HHS (United States)

T32 GM008666 NIGMS NIH HHS (United States)

T32 GM087237 NIGMS NIH HHS (United States)

U54 HG007005 NHGRI NIH HHS (United States)

U54 NS091046 NINDS NIH HHS (United States)

R01 NS075449 NINDS NIH HHS (United States)

R35 NS097974 NINDS NIH HHS (United States)

Linked Datasets (10)

GSE86462 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_iPSC_MN_Stress]

Homo sapiens

GSE86223 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_iPSC_MN_ASO]

Homo sapiens

GSE86041 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [iCLIP-seq]

Mus musculus

2 data files

File	Type	Size
2_NoIndex_L002_R1.R16.randomer.fastq.gz	RIP-Seq	2.2 GB
2_NoIndex_L002_R1.R16.randomer.fastq.gz	RIP-Seq	2.2 GB

GSE86038 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_Fibs_2]

Homo sapiens

GSE86464 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons

Mus musculus

GSE86218 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_human_Fibs_1]

Homo sapiens

GSE86227 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_small_rnaseq]

Mus musculus

24 data files

File	Type	Size
B7P80-501-1_S7_L001_R1_001.fastq	ncRNA-Seq	27.6 MB
B7P80-501-1_S7_L001_R1_001.fastq	ncRNA-Seq	27.6 MB
B7P80-501-2_S1_L001_R1_001.fastq	ncRNA-Seq	20.9 MB
B7P80-501-2_S1_L001_R1_001.fastq	ncRNA-Seq	20.9 MB
B7P80-501-3_S3_L001_R1_001.fastq	ncRNA-Seq	20.5 MB
B7P80-501-3_S3_L001_R1_001.fastq	ncRNA-Seq	20.5 MB
B7P80-A1_S2_L001_R1_001.fastq	ncRNA-Seq	24.5 MB
B7P80-A1_S2_L001_R1_001.fastq	ncRNA-Seq	24.5 MB
B7P80-A2_S9_L001_R1_001.fastq	ncRNA-Seq	21.6 MB
B7P80-A2_S9_L001_R1_001.fastq	ncRNA-Seq	21.6 MB
B7P80-A3_S11_L001_R1_001.fastq	ncRNA-Seq	21.1 MB
B7P80-A3_S11_L001_R1_001.fastq	ncRNA-Seq	21.1 MB
B7P80-C-1_S4_L001_R1_001.fastq	ncRNA-Seq	20.3 MB
B7P80-C-1_S4_L001_R1_001.fastq	ncRNA-Seq	20.3 MB
B7P80-C-2_S5_L001_R1_001.fastq	ncRNA-Seq	18.1 MB
B7P80-C-2_S5_L001_R1_001.fastq	ncRNA-Seq	18.1 MB
B7P80-C-3_S6_L001_R1_001.fastq	ncRNA-Seq	21.2 MB
B7P80-C-3_S6_L001_R1_001.fastq	ncRNA-Seq	21.2 MB
B7P80-D1_S12_L001_R1_001.fastq	ncRNA-Seq	22.6 MB
B7P80-D1_S12_L001_R1_001.fastq	ncRNA-Seq	22.6 MB
B7P80-D2_S13_L001_R1_001.fastq	ncRNA-Seq	20.3 MB
B7P80-D2_S13_L001_R1_001.fastq	ncRNA-Seq	20.3 MB
B7P80-D3_S8_L001_R1_001.fastq	ncRNA-Seq	35.8 MB
B7P80-D3_S8_L001_R1_001.fastq	ncRNA-Seq	35.8 MB

GSE86224 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_Arrays_mouse_SC]

Mus musculus

GSE86043 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_RNA-seq_mouse_SC]

Mus musculus

14 data files

File	Type	Size
A1-SC_ATTACTCG_L002_R1.fastq.gz	RNA-Seq	5.8 GB
A1-SC_ATTACTCG_L002_R1.fastq.gz	RNA-Seq	5.8 GB
A2-SC_TCCGGAGA_L002_R1.fastq.gz	RNA-Seq	5.2 GB
A2-SC_TCCGGAGA_L002_R1.fastq.gz	RNA-Seq	5.2 GB
A3-SC_CGCTCATT_L002_R1.fastq.gz	RNA-Seq	467.8 MB
A3-SC_CGCTCATT_L002_R1.fastq.gz	RNA-Seq	467.8 MB
D1-SC_GAGATTCC_L002_R1.fastq.gz	RNA-Seq	1.3 GB
D1-SC_GAGATTCC_L002_R1.fastq.gz	RNA-Seq	1.3 GB
D2-SC_ATTCAGAA-TATAGCCT_L003_R1.fastq.gz	RNA-Seq	1.7 GB
D2-SC_ATTCAGAA-TATAGCCT_L003_R1.fastq.gz	RNA-Seq	1.7 GB
D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz	RNA-Seq	725.8 MB
D3-SC_GAATTCGT-TATAGCCT_L003_R1.fastq.gz	RNA-Seq	725.8 MB
D4-SC_CTGAAGCT-TATAGCCT_L003_R1.fastq.gz	RNA-Seq	1.2 GB
D4-SC_CTGAAGCT-TATAGCCT_L003_R1.fastq.gz	RNA-Seq	1.2 GB

GSE86040 GSE via ncbi_elink

GEO

HNRNPA2B1 regulates alternative RNA processing in the nervous system and accumulates in granules in ALS IPSC-derived motor neurons [hnRNPA2B1_eCLIP_human_iPSC_MN]

Homo sapiens

42 data files

File	Type	Size
F1_IN_A2B1_ATTACTCG-TATAGCCT_L008_R1.unassigned.randomer.fa…	RIP-Seq	606.4 MB
F1_IN_A2B1_ATTACTCG-TATAGCCT_L008_R1.unassigned.randomer.fa…	RIP-Seq	606.4 MB
F1_IP_A2B1_TCCGGAGA-TATAGCCT_L008_R1.A01_F1_IP_mnCLIP_A2B1_…	RIP-Seq	225.5 MB
F1_IP_A2B1_TCCGGAGA-TATAGCCT_L008_R1.A01_F1_IP_mnCLIP_A2B1_…	RIP-Seq	225.5 MB
F1_IP_A2B1_TCCGGAGA-TATAGCCT_L008_R1.B06_F1_IP_mnCLIP_A2B1_…	RIP-Seq	156.4 MB
F1_IP_A2B1_TCCGGAGA-TATAGCCT_L008_R1.B06_F1_IP_mnCLIP_A2B1_…	RIP-Seq	156.4 MB
F2_IN_A2B1_CGCTCATT-TATAGCCT_L008_R1.unassigned.randomer.fa…	RIP-Seq	506.5 MB
F2_IN_A2B1_CGCTCATT-TATAGCCT_L008_R1.unassigned.randomer.fa…	RIP-Seq	506.5 MB
F2_IP_A2B1_GAGATTCC-TATAGCCT_L008_R1.C01_F2_IP_mnCLIP_A2B1_…	RIP-Seq	245.9 MB
F2_IP_A2B1_GAGATTCC-TATAGCCT_L008_R1.C01_F2_IP_mnCLIP_A2B1_…	RIP-Seq	245.9 MB
F2_IP_A2B1_GAGATTCC-TATAGCCT_L008_R1.D08fixed_F2_IP_mnCLIP_…	RIP-Seq	138.8 MB
F2_IP_A2B1_GAGATTCC-TATAGCCT_L008_R1.D08fixed_F2_IP_mnCLIP_…	RIP-Seq	138.8 MB
F3_IN_A2B1_ATTCAGAA-TATAGCCT_L008_R1.unassigned.randomer.fa…	RIP-Seq	733.5 MB
F3_IN_A2B1_ATTCAGAA-TATAGCCT_L008_R1.unassigned.randomer.fa…	RIP-Seq	733.5 MB
F3_IP_A2B1_GAATTCGT-TATAGCCT_L008_R1.A01_F3_IP_mnCLIP_A2B1_…	RIP-Seq	140.0 MB
F3_IP_A2B1_GAATTCGT-TATAGCCT_L008_R1.A01_F3_IP_mnCLIP_A2B1_…	RIP-Seq	140.0 MB
F3_IP_A2B1_GAATTCGT-TATAGCCT_L008_R1.B06_F3_IP_mnCLIP_A2B1_…	RIP-Seq	88.0 MB
F3_IP_A2B1_GAATTCGT-TATAGCCT_L008_R1.B06_F3_IP_mnCLIP_A2B1_…	RIP-Seq	88.0 MB
F4_IN_A2B1_ATTACTCG-ATAGAGGC_L008_R1.unassigned.randomer.fa…	RIP-Seq	735.2 MB
F4_IN_A2B1_ATTACTCG-ATAGAGGC_L008_R1.unassigned.randomer.fa…	RIP-Seq	735.2 MB
F4_IP_A2B1_TCCGGAGA-ATAGAGGC_L008_R1.C01_F4_IP_mnCLIP_A2B1_…	RIP-Seq	392.8 MB
F4_IP_A2B1_TCCGGAGA-ATAGAGGC_L008_R1.C01_F4_IP_mnCLIP_A2B1_…	RIP-Seq	392.8 MB
F4_IP_A2B1_TCCGGAGA-ATAGAGGC_L008_R1.D08fixed_F4_IP_mnCLIP_…	RIP-Seq	122.7 MB
F4_IP_A2B1_TCCGGAGA-ATAGAGGC_L008_R1.D08fixed_F4_IP_mnCLIP_…	RIP-Seq	122.7 MB
F5_IN_A2B1_CGCTCATT-ATAGAGGC_L008_R1.unassigned.randomer.fa…	RIP-Seq	447.8 MB
F5_IN_A2B1_CGCTCATT-ATAGAGGC_L008_R1.unassigned.randomer.fa…	RIP-Seq	447.8 MB
F5_IP_A2B1_GAGATTCC-ATAGAGGC_L008_R1.A01_F5_IP_mnCLIP_A2B1_…	RIP-Seq	282.0 MB
F5_IP_A2B1_GAGATTCC-ATAGAGGC_L008_R1.A01_F5_IP_mnCLIP_A2B1_…	RIP-Seq	282.0 MB
F5_IP_A2B1_GAGATTCC-ATAGAGGC_L008_R1.B06_F5_IP_mnCLIP_A2B1_…	RIP-Seq	108.2 MB
F5_IP_A2B1_GAGATTCC-ATAGAGGC_L008_R1.B06_F5_IP_mnCLIP_A2B1_…	RIP-Seq	108.2 MB
F6_IN_A2B1_ATTCAGAA-ATAGAGGC_L008_R1.unassigned.randomer.fa…	RIP-Seq	340.9 MB
F6_IN_A2B1_ATTCAGAA-ATAGAGGC_L008_R1.unassigned.randomer.fa…	RIP-Seq	340.9 MB
F6_IP_A2B1_GAATTCGT-ATAGAGGC_L008_R1.C01_F6_IP_mnCLIP_A2B1_…	RIP-Seq	315.6 MB
F6_IP_A2B1_GAATTCGT-ATAGAGGC_L008_R1.C01_F6_IP_mnCLIP_A2B1_…	RIP-Seq	315.6 MB
F6_IP_A2B1_GAATTCGT-ATAGAGGC_L008_R1.D08fixed_F6_IP_mnCLIP_…	RIP-Seq	111.7 MB
F6_IP_A2B1_GAATTCGT-ATAGAGGC_L008_R1.D08fixed_F6_IP_mnCLIP_…	RIP-Seq	111.7 MB
F7_IN_IgG_ATTACTCG-CCTATCCT_L008_R1.unassigned.randomer.fas…	RIP-Seq	446.3 MB
F7_IN_IgG_ATTACTCG-CCTATCCT_L008_R1.unassigned.randomer.fas…	RIP-Seq	446.3 MB
F7_IP_IgG_ATTCAGAA-CCTATCCT_L008_R1.A01_F7_IP_mnCLIP_IgG_hi…	RIP-Seq	102.4 KB
F7_IP_IgG_ATTCAGAA-CCTATCCT_L008_R1.A01_F7_IP_mnCLIP_IgG_hi…	RIP-Seq	102.4 KB
F7_IP_IgG_ATTCAGAA-CCTATCCT_L008_R1.B06_F7_IP_mnCLIP_IgG_hi…	RIP-Seq	112.6 KB
F7_IP_IgG_ATTCAGAA-CCTATCCT_L008_R1.B06_F7_IP_mnCLIP_IgG_hi…	RIP-Seq	112.6 KB