GSE124714

GSE GEO

View on GEO Export SRA CSV

The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics

Organism: 6239

Platform: GPL13657

Samples: 2

Experiment Types:

Other

Submitted: Jan 06 2019

Last Updated: Jan 25 2020

Status: Public on Jan 23 2020

Contact: Ngang Heok,,Tang (UC San Diego)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA513199 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP176284

Summary

mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for degradation, yet it remains poorly understood how mRNA decay factors function in vivo to regulate specific cellular processes. Here we show that mRNA decay factors form cytoplasmic puncta in C. elegans neurons and have opposing roles in axon maintenance and regrowth. While the decapping enzymes DCAP-1/DCP1 and DCAP-2/DCP2 regulate developmental axon guidance and promote axon regrowth upon injury, the translational repressors CAR-1/LSM14 and CGH-1/DDX6 regulate axon maintenance and inhibit axon regrowth in adult animals. We identified mRNA targets of CAR-1 in neurons and found that the mitochondrial calcium uptake regulator micu-1 is repressed by CAR-1. We show that axon injury triggers a transient mitochondrial calcium influx via the MCU-1 uniporter that is more sustained in car-1 loss of function mutants. The enhanced axon regrowth and defective axon maintenance of car-1 mutants are dependent on MICU-1 function. Our results uncover specific roles for mRNA decay regulators in neurons and reveal a novel pathway that controls axon regrowth through mitochondrial calcium uptake.

Overall Design

seCLIP-seq in C. elegans strains CZ25180 and CZ26430

Analysis (14 steps)

View Data Processing

Processing steps for GSE124714

(Using CZ25180_S1_L008_R1_001.fastq.gz as an example starting fastq file): umi_tools extract --stdin CZ25180_S1_L008_R1_001.fastq.gz --bc-pattern NNNNNNNNNN --log CAR1.CZ25180_IP.---.--.metrics CAR1 --stdout CAR1.CZ25180_IP.umi.r1.fq
cutadapt -O \ 1 \ -f \ fastq \ --match-read-wildcards \ --times \ 1 \ -e \ 0.1 \ --quality-cutoff \ 6 \ -m \ 18 \ -o \ CAR1.CZ25180_IP.umi.r1Tr.fq \ '-a AGATCGGAAGAGCAC' \ '-a GATCGGAAGAGCACA' \ '-a ATCGGAAGAGCACAC' \ '-a TCGGAAGAGCACACG' \ '-a CGGAAGAGCACACGT' \ '-a GGAAGAGCACACGTC' \ '-a GAAGAGCACACGTCT' \ '-a AAGAGCACACGTCTG' \ '-a AGAGCACACGTCTGA' \ '-a GAGCACACGTCTGAA' \ '-a AGCACACGTCTGAAC' \ '-a GCACACGTCTGAACT' \ '-a CACACGTCTGAACTC' \ '-a ACACGTCTGAACTCC' \ '-a CACGTCTGAACTCCA' \ '-a ACGTCTGAACTCCAG' \ '-a CGTCTGAACTCCAGT' \ '-a GTCTGAACTCCAGTC' \ '-a TCTGAACTCCAGTCA' \ '-a CTGAACTCCAGTCAC' \ CAR1.CZ25180_IP.umi.r1.fq
cutadapt \ -O \ 5 \ -f \ fastq \ --match-read-wildcards \ --times \ 1 \ -e \ 0.1 \ --quality-cutoff \ 6 \ -m \ 18 \ -o \ CAR1.CZ25180_IP.umi.r1TrTr.fq \ -a AGATCGGAAGAGCAC \ -a GATCGGAAGAGCACA \ -a ATCGGAAGAGCACAC \ -a TCGGAAGAGCACACG \ -a CGGAAGAGCACACGT \ -a GGAAGAGCACACGTC \ -a GAAGAGCACACGTCT \ -a AAGAGCACACGTCTG \ -a AGAGCACACGTCTGA \ -a GAGCACACGTCTGAA \ -a AGCACACGTCTGAAC \ -a GCACACGTCTGAACT \ -a CACACGTCTGAACTC \ -a ACACGTCTGAACTCC \ -a CACGTCTGAACTCCA \ -a ACGTCTGAACTCCAG \ -a CGTCTGAACTCCAGT \ -a GTCTGAACTCCAGTC \ -a TCTGAACTCCAGTCA \ -a CTGAACTCCAGTCAC \ CAR1.CZ25180_IP.umi.r1Tr.fq
fastq-sort --id CAR1.CZ25180_IP.umi.r1TrTr.fq > CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq
STAR \ --alignEndsType \ EndToEnd \ --genomeDir \ RepBase18.05.STAR \ --genomeLoad \ NoSharedMemory \ --outBAMcompression \ 10 \ --outFileNamePrefix \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STAR \ --outFilterMultimapNmax \ 30 \ --outFilterMultimapScoreRange \ 1 \ --outFilterScoreMin \ 10 \ --outFilterType \ BySJout \ --outReadsUnmapped \ Fastx \ --outSAMattrRGline \ ID:foo \ --outSAMattributes \ All \ --outSAMmode \ Full \ --outSAMtype \ BAM \ Unsorted \ --outSAMunmapped \ Within \ --outStd \ Log \ --readFilesIn \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.fq \ --runMode \ alignReads \ --runThreadN \ 8
STAR \ --alignEndsType \ EndToEnd \ --genomeDir \ ce10.STAR \ --genomeLoad \ NoSharedMemory \ --outBAMcompression \ 10 \ --outFileNamePrefix \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STAR \ --outFilterMultimapNmax \ 1 \ --outFilterMultimapScoreRange \ 1 \ --outFilterScoreMin \ 10 \ --outFilterType \ BySJout \ --outReadsUnmapped \ Fastx \ --outSAMattrRGline \ ID:foo \ --outSAMattributes \ All \ --outSAMmode \ Full \ --outSAMtype \ BAM \ Unsorted \ --outSAMunmapped \ Within \ --outStd \ Log \ --readFilesIn \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.fq \ --runMode \ alignReads \ --runThreadN \ 8
umi_tools \ dedup \ -I \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.bam \ --output-stats \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo \ -S \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam
sort \ -o \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDupSo.bam \ CAR1.CZ25180_IP.umi.r1TrTr.sorted.STARUnmapped.out.sorted.STARAligned.outSo.rmDup.bam

Showing first 8 steps.

Supplementary Files (1)

GSE124714_RAW.tar Download

GEO Samples (2)

GSM3543766 GSM3543767

SRA Experiments (2) and Runs (2)

Total: 2721 MB

SRX5210676 SRP176284 OTHER SINGLE

GSM3543766: CAR-1(FL); Caenorhabditis elegans; OTHER

Sample: SRS4214991

BioProject: PRJNA513199

BioSample: SAMN10698044

Platform: ILLUMINA

Instrument: Illumina HiSeq 2000

Organism: Caenorhabditis elegans

Sample attributes

source_name: CZ25180

antibody: GFP-trap

antibody manufacturer: antibody manufacturer: Chromotek

catalog number: antibody catalog #: gta-10

Original files (1)

CZ25180

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR8401420	43905923	3292944225	1099.56	CZ25180_S1_L008_R1_001.fastq.gz, SRR8401420, SRR8401420.sralite	SRA

SRX5210677 SRP176284 OTHER SINGLE

GSM3543767: CAR-1(dSm); Caenorhabditis elegans; OTHER

Sample: SRS4214992

BioProject: PRJNA513199

BioSample: SAMN10698043

Platform: ILLUMINA

Instrument: Illumina HiSeq 2000

Organism: Caenorhabditis elegans

Sample attributes

source_name: CZ26430

antibody: GFP-trap

antibody manufacturer: antibody manufacturer: Chromotek

catalog number: antibody catalog #: gta-10

Original files (1)

CZ26430

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR8401421	64702729	4852704675	1621.27	CZ26430_S2_L008_R1_001.fastq.gz, SRR8401421, SRR8401421.sralite	SRA

Linked Publications (1)

The mRNA Decay Factor CAR-1/LSM14 Regulates Axon Regeneration via Mitochondrial Calcium Dynamics.

Current biology : CB · 2020

Data Files (2)

Select	Accession	File Name	Stored Type	Output Type	Mapping Assembly	Size	Download
	—	CZ25180_S1_L008_R1_001.fastq.gz	OTHER			1.1 GB	link
	—	CZ26430_S2_L008_R1_001.fastq.gz	OTHER			1.6 GB	link