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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.

Stephanie C Huelga, Anthony Q Vu, Justin D Arnold, Tiffany Y Liang, Patrick P Liu, Bernice Y Yan, John Paul Donohue, Lily Shiue, Shawn Hoon, Sydney Brenner, Manuel Ares, Gene W Yeo
Cell reports · 2012 · Vol. 1 (2) · pp. 167-78
PubMed DOI PMC Full Text

Abstract

Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq), and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and autoregulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.

Publication Types

["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S."]

Keywords

[]

MeSH Terms

["Alternative Splicing", "Base Sequence", "Binding Sites", "Blotting, Western", "Exons", "Fibroblasts", "Genes, Neoplasm", "Genome, Human", "HEK293 Cells", "Heterogeneous-Nuclear Ribonucleoproteins", "Humans", "Molecular Sequence Data", "Nucleotide Motifs", "Oligonucleotide Array Sequence Analysis", "Organ Specificity", "Protein Binding", "Protein Interaction Mapping", "RNA Precursors", "Reproducibility of Results", "Reverse Transcriptase Polymerase Chain Reaction"]

Funding

R01 HG004659 NHGRI NIH HHS (United States)
R01 NS075449 NINDS NIH HHS (United States)
HG004659 NHGRI NIH HHS (United States)
R01 GM084317 NIGMS NIH HHS (United States)
GM084317 NIGMS NIH HHS (United States)

Linked Datasets (4)

GSE34996 GSE via ncbi_elink
GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins

Homo sapiens
GSE34995 GSE via ncbi_elink
GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)

Homo sapiens
62 data files
FileTypeSize
control_293T_RNAseq_1_sequence.txt RNA-Seq 485.3 MB
control_293T_RNAseq_1_sequence.txt RNA-Seq 485.3 MB
control_293T_RNAseq_2_sequence.txt RNA-Seq 397.3 MB
control_293T_RNAseq_2_sequence.txt RNA-Seq 397.3 MB
control_293T_RNAseq_3_sequence.txt RNA-Seq 557.7 MB
control_293T_RNAseq_3_sequence.txt RNA-Seq 557.7 MB
control_293T_RNAseq_4_sequence.txt RNA-Seq 547.7 MB
control_293T_RNAseq_4_sequence.txt RNA-Seq 547.7 MB
control_293T_RNAseq_5_sequence.txt RNA-Seq 751.5 MB
control_293T_RNAseq_5_sequence.txt RNA-Seq 751.5 MB
control_293T_RNAseq_6_sequence.txt RNA-Seq 790.2 MB
control_293T_RNAseq_6_sequence.txt RNA-Seq 790.2 MB
hnRNPA1_293T_RNAseq_KD1a_sequence.txt RNA-Seq 266.9 MB
hnRNPA1_293T_RNAseq_KD1a_sequence.txt RNA-Seq 266.9 MB
hnRNPA1_293T_RNAseq_KD2a_sequence.txt RNA-Seq 315.5 MB
hnRNPA1_293T_RNAseq_KD2a_sequence.txt RNA-Seq 315.5 MB
hnRNPA1_293T_RNAseq_KD3a_sequence.txt RNA-Seq 258.7 MB
hnRNPA1_293T_RNAseq_KD3a_sequence.txt RNA-Seq 258.7 MB
hnRNPA1_293T_RNAseq_KD3b_sequence.txt RNA-Seq 1.2 GB
hnRNPA1_293T_RNAseq_KD3b_sequence.txt RNA-Seq 1.2 GB
hnRNPA1_293T_RNAseq_KD3c_sequence.txt RNA-Seq 760.1 MB
hnRNPA1_293T_RNAseq_KD3c_sequence.txt RNA-Seq 760.1 MB
hnRNPA1_293T_RNAseq_KD3d_sequence.txt RNA-Seq 769.1 MB
hnRNPA2B1_293T_RNAseq_KD1a_sequence.txt RNA-Seq 629.9 MB
hnRNPA2B1_293T_RNAseq_KD1a_sequence.txt RNA-Seq 629.9 MB
hnRNPA2B1_293T_RNAseq_KD2a_sequence.txt RNA-Seq 447.6 MB
hnRNPA2B1_293T_RNAseq_KD2a_sequence.txt RNA-Seq 447.6 MB
hnRNPF_293T_RNAseq_KD1a_sequence.txt RNA-Seq 446.9 MB
hnRNPF_293T_RNAseq_KD1a_sequence.txt RNA-Seq 446.9 MB
hnRNPF_293T_RNAseq_KD1b_sequence.txt RNA-Seq 720.1 MB
hnRNPF_293T_RNAseq_KD1b_sequence.txt RNA-Seq 720.1 MB
hnRNPF_293T_RNAseq_KD2a_sequence.txt RNA-Seq 670.7 MB
hnRNPF_293T_RNAseq_KD2a_sequence.txt RNA-Seq 670.7 MB
hnRNPF_293T_RNAseq_KD2b_sequence.txt RNA-Seq 779.5 MB
hnRNPF_293T_RNAseq_KD2b_sequence.txt RNA-Seq 779.5 MB
hnRNPF_293T_RNAseq_KD2c_sequence.txt RNA-Seq 767.9 MB
hnRNPF_293T_RNAseq_KD2c_sequence.txt RNA-Seq 767.9 MB
hnRNPH1_293T_RNAseq_KD1a_sequence.txt RNA-Seq 688.8 MB
hnRNPH1_293T_RNAseq_KD1a_sequence.txt RNA-Seq 688.8 MB
hnRNPH1_293T_RNAseq_KD2a_sequence.txt RNA-Seq 1.2 GB
hnRNPM_293T_RNAseq_KD1a_sequence.txt RNA-Seq 340.2 MB
hnRNPM_293T_RNAseq_KD1a_sequence.txt RNA-Seq 340.2 MB
hnRNPM_293T_RNAseq_KD1b_sequence.txt RNA-Seq 1.1 GB
hnRNPM_293T_RNAseq_KD1b_sequence.txt RNA-Seq 1.1 GB
hnRNPM_293T_RNAseq_KD1c_sequence.txt RNA-Seq 688.6 MB
hnRNPM_293T_RNAseq_KD1c_sequence.txt RNA-Seq 688.6 MB
hnRNPM_293T_RNAseq_KD1d_sequence.txt RNA-Seq 684.9 MB
hnRNPM_293T_RNAseq_KD1d_sequence.txt RNA-Seq 684.9 MB
hnRNPM_293T_RNAseq_KD2a_sequence.txt RNA-Seq 324.7 MB
hnRNPM_293T_RNAseq_KD2a_sequence.txt RNA-Seq 324.7 MB
hnRNPM_293T_RNAseq_KD2b_sequence.txt RNA-Seq 320.6 MB
hnRNPU_293T_RNAseq_KD1a_sequence.txt RNA-Seq 449.8 MB
hnRNPU_293T_RNAseq_KD1a_sequence.txt RNA-Seq 449.8 MB
hnRNPU_293T_RNAseq_KD1b_sequence.txt RNA-Seq 1.2 GB
hnRNPU_293T_RNAseq_KD1b_sequence.txt RNA-Seq 1.2 GB
hnRNPU_293T_RNAseq_KD2a_sequence.txt RNA-Seq 762.2 MB
hnRNPU_293T_RNAseq_KD2a_sequence.txt RNA-Seq 762.2 MB
hnRNPU_293T_RNAseq_KD2b_sequence.txt RNA-Seq 3.2 GB
SRR398215 RNA-Seq 769.1 MB
SRR398224 RNA-Seq 1.2 GB
SRR398230 RNA-Seq 320.6 MB
SRR398234 RNA-Seq 3.2 GB
GSE34992 GSE via ncbi_elink
GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

Homo sapiens
GSE34993 GSE via ncbi_elink
GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)

Homo sapiens
30 data files
FileTypeSize
hnRNPA1_293T_CLIPseq_1_sequence.txt RNA-Seq 54.6 MB
hnRNPA1_293T_CLIPseq_1_sequence.txt RNA-Seq 54.6 MB
hnRNPA1_293T_CLIPseq_2_sequence.txt RNA-Seq 83.2 MB
hnRNPA1_293T_CLIPseq_3_sequence.txt RNA-Seq 80.7 MB
hnRNPA1_293T_CLIPseq_3_sequence.txt RNA-Seq 80.7 MB
hnRNPA1_293T_CLIPseq_4_sequence.txt RNA-Seq 409.6 KB
hnRNPA1_293T_CLIPseq_4_sequence.txt RNA-Seq 409.6 KB
hnRNPA2B1_293T_CLIPseq_1_sequence.txt RNA-Seq 475.5 MB
hnRNPA2B1_293T_CLIPseq_1_sequence.txt RNA-Seq 475.5 MB
HnRNPF_293T_CLIPseq_1_sequence.txt RNA-Seq 145.5 MB
HnRNPF_293T_CLIPseq_1_sequence.txt RNA-Seq 145.5 MB
HnRNPF_293T_CLIPseq_2_sequence.txt RNA-Seq 155.0 MB
HnRNPF_293T_CLIPseq_3_sequence.txt RNA-Seq 216.1 MB
HnRNPF_293T_CLIPseq_4_sequence.txt RNA-Seq 418.5 MB
HnRNPM_293T_CLIPseq_1_sequence.txt RNA-Seq 144.1 MB
HnRNPM_293T_CLIPseq_1_sequence.txt RNA-Seq 144.1 MB
HnRNPM_293T_CLIPseq_2_sequence.txt RNA-Seq 140.6 MB
HnRNPM_293T_CLIPseq_2_sequence.txt RNA-Seq 140.6 MB
HnRNPU_293T_CLIPseq_1_sequence.txt RNA-Seq 149.6 MB
HnRNPU_293T_CLIPseq_1_sequence.txt RNA-Seq 149.6 MB
HnRNPU_293T_CLIPseq_2_sequence.txt RNA-Seq 86.0 MB
HnRNPU_293T_CLIPseq_2_sequence.txt RNA-Seq 86.0 MB
HnRNPU_293T_CLIPseq_3_sequence.txt RNA-Seq 64.8 MB
HnRNPU_293T_CLIPseq_3_sequence.txt RNA-Seq 64.8 MB
HnRNPU_293T_CLIPseq_4_sequence.txt RNA-Seq 392.5 MB
HnRNPU_293T_CLIPseq_4_sequence.txt RNA-Seq 392.5 MB
SRR398196 RNA-Seq 83.2 MB
SRR398201 RNA-Seq 155.0 MB
SRR398202 RNA-Seq 216.1 MB
SRR398203 RNA-Seq 418.5 MB

Analysis Pipelines (4)

GSE34992 Microarray Data Processing 2 steps
Microarray geo_data_processing GSE34992
GSE34993 CLIP-seq Data Processing 2 steps
CLIP-seq geo_data_processing GSE34993
GSE34995 RNA-seq Data Processing 2 steps
RNA-seq geo_data_processing GSE34995
GSE34996 Microarray Data Processing 2 steps
Microarray geo_data_processing GSE34996