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Folder iconSplicing and Polyadenylation regulation by TDP-43

Rahul Arora
June 13, 2019
Many RNA-binding proteins (RBPs) regulate both alternative exons and poly(A) site selection. To understand their regulatory principles, we developed expressRNA, a web platform encompassing computational tools for integration of iCLIP and RNA motif analyses with RNA-seq and 3′ mRNA sequencing. This reveals at nucleotide resolution the “RNA maps” describing how the RNA binding positions of RBPs relate to their regulatory functions. We use this approach to examine how TDP-43, an RBP involved in several neurodegenerative diseases, binds around its regulated poly(A) sites. Binding close to the poly(A) site generally represses, whereas binding further downstream enhances use of the site, which is similar to TDP-43 binding around regulated exons. Our RNAmotifs2 software also identifies sequence motifs that cluster together with the binding motifs of TDP-43. We conclude that TDP-43 directly regulates diverse types of pre-mRNA processing according to common position-dependent principles.

Un1510_JU_1_S0_L001_R1_001.fastq.gz

FASTQ file (single-end)
fastqc
Directory
Un1510_JU_1_S0_L001_R1_001.fastq.gz
6.74 GB
Un1510_JU_1_S0_L001_R1_001_fastqc.zip
514.58 kB
stderr.txt
1.17 kB

TARDBP_293Flp_TARDBP_LC_flag_GFP_IP_20151023_JU1_1

FASTQ file (single-end)
fastqc
Directory
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1.fastq.gz
226.02 MB
stderr.txt
1.64 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_fastqc.zip
440.04 kB
Paraclu
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_peaks.bed.gz
288.29 kB
iCount RNA-maps
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single.tar.gz
1.79 MB
K-mers
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1.tar.gz
491.10 kB
Cutadapt (single-end)
report.txt
687 B
fastqc
Directory
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed.fastq.gz
229.67 MB
STAR
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed.bam.bai
3.61 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed.bam
391.16 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_unmapped.out.mate1.fastq.gz
19.98 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_stats.txt
1.81 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_SJ.out.tab
1.00 MB
iCount xlsites
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_singleAndMulti.bed.gz
31.30 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_reads_single.bed.gz
21.03 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single.bed.gz
20.07 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_skipped.bam
3.76 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single.bedgraph
95.25 MB
iCount summary
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_summary_type.tsv
441 B
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_summary_subtype.tsv
1.01 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_summary_gene.tsv
1.92 MB

No Sample

FASTQ file (single-end)
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_fastqc.zip
446.02 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1.fastq.gz
679.66 MB
fastqc
Directory
stderr.txt
1.68 kB
Upload iCount sample annotation
TDP43_28467899_annotation_sheet.xlsx
14.46 kB
TDP43_28467899_annotation_sheet.tab.gz
886 B
FASTQ file (single-end)
fastqc
Directory
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1.fastq.gz
226.02 MB
stderr.txt
1.64 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_fastqc.zip
440.04 kB
Paraclu
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_peaks.bed.gz
288.29 kB
FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch.fastq.gz
5.20 GB
demux_nomatch_fastqc.zip
525.61 kB
FASTQ file (single-end)
fastqc
Directory
Un1510_JU_1_S0_L001_R1_001.fastq.gz
6.74 GB
Un1510_JU_1_S0_L001_R1_001_fastqc.zip
514.58 kB
stderr.txt
1.17 kB
iCount demultiplex (from annotation file)
demultiplexing_stats.txt
308 B
iCount RNA-maps
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single.tar.gz
1.79 MB
K-mers
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1.tar.gz
491.10 kB
iCount RNA-maps
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single.tar.gz
2.95 MB
Paraclu
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_peaks.bed.gz
948.74 kB
Cutadapt (single-end)
report.txt
687 B
fastqc
Directory
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed.fastq.gz
229.67 MB
K-mers
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1.tar.gz
579.51 kB
Cutadapt (single-end)
fastqc
Directory
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed.fastq.gz
690.09 MB
report.txt
685 B
STAR
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed.bam.bai
3.61 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed.bam
391.16 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_unmapped.out.mate1.fastq.gz
19.98 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_stats.txt
1.81 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_SJ.out.tab
1.00 MB
STAR
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_unmapped.out.mate1.fastq.gz
66.66 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_stats.txt
1.81 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed.bam.bai
2.93 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed.bam
1.12 GB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_SJ.out.tab
2.66 MB
iCount xlsites
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_singleAndMulti.bed.gz
31.30 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_reads_single.bed.gz
21.03 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single.bed.gz
20.07 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_skipped.bam
3.76 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single.bedgraph
95.25 MB
iCount xlsites
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_skipped.bam
4.44 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_singleAndMulti.bed.gz
84.31 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single.bed.gz
54.44 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_reads_single.bed.gz
56.78 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single.bedgraph
261.04 MB
iCount summary
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_summary_type.tsv
441 B
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_summary_subtype.tsv
1.01 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1-1_trimmed_single_summary_gene.tsv
1.92 MB
iCount summary
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_summary_subtype.tsv
1.02 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_summary_type.tsv
446 B
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_summary_gene.tsv
2.38 MB

TARDBP_293Flp_TARDBP_LC_flag_GFP_IP_20151023_JU1

FASTQ file (single-end)
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1.fastq.gz
679.66 MB
fastqc
Directory
stderr.txt
1.68 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_fastqc.zip
446.02 kB
iCount RNA-maps
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single.tar.gz
2.95 MB
Paraclu
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_peaks.bed.gz
948.74 kB
K-mers
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1.tar.gz
579.51 kB
Cutadapt (single-end)
fastqc
Directory
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed.fastq.gz
690.09 MB
report.txt
685 B
STAR
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_unmapped.out.mate1.fastq.gz
66.66 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_stats.txt
1.81 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed.bam.bai
2.93 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed.bam
1.12 GB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_SJ.out.tab
2.66 MB
iCount xlsites
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_skipped.bam
4.44 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_singleAndMulti.bed.gz
84.31 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single.bed.gz
54.44 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_reads_single.bed.gz
56.78 MB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single.bedgraph
261.04 MB
iCount summary
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_summary_subtype.tsv
1.02 kB
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_summary_type.tsv
446 B
tardbp-293flp-tardbp-lc-flag-gfp-ip-20151023-ju1_trimmed_single_summary_gene.tsv
2.38 MB

demux_nomatch.fastq.gz

FASTQ file (single-end)
fastqc
Directory
stderr.txt
935 B
demux_nomatch.fastq.gz
5.20 GB
demux_nomatch_fastqc.zip
525.61 kB