GSE193134

GSE GEO

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LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function

Organism: Homo sapiens

Platform: GPL20301

Samples: 4

Experiment Types:

Other

Submitted: Jan 06 2022

Last Updated: Mar 12 2024

Status: Public on Mar 11 2024

Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA795057

Summary

Mitochondrial associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples described, we set out to identify RBPs that post-transcriptionally regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our analysis of RNA-target sets of RBPs made available by ENCODE identified several RBPs with a preference for binding NEMmRNAs, of which we selected LARP4, a La RBP family member, for further study. We show that LARP4âs RNA-target set is particularly enriched in mRNAs that encode for respiratory chain complex proteins (RCCPs) and mitochondrial ribosome proteins (MRPs) across multiple human cell lines. CRISPR knockout cells in conjunction with quantitative proteomics show that protein levels of RCCPs and MRPs are significantly reduced upon loss of LARP4. Furthermore, we show that LARP4 depletion reduces mitochondrial function, and this phenotype is ameliorated by LARP4 re-expression. Our findings shed light onto a novel function for LARP4 as an RBP that binds to NEMmRNAs to promote mitochondrial respiratory function.

Overall Design

Identification of LARP4 targets using eCLIP-seq in HEK293 cell line

Analysis (18 steps)

View Data Processing

Processing steps for GSE193134

Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0).
Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14).
Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed again with cutadapt (1.14) to remove double-ligation events.
Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Trimmed and filtered reads were then mapped with STAR (2.7.6a) against a repeat element database (RepBase 18.05).
Args: --runThreadN 16 \ --genomeDir human_repbase \ --readFilesIn path/to/read1 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd

Showing first 8 steps.

Supplementary Files (2)

GSE193134_LARP4_hek_WT.bed.gz Download

GSE193134_RAW.tar Download

GEO Samples (4)

GSM5773932 GSM5773933 GSM5773934 GSM5773935

Dataset Citations (1)

LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function.

PMID 38164626 · 2024 · RNA (New York, N.Y.)

Benjamin M Lewis, Chae Yun Cho, Hsuan-Lin Her, Orel Mizrahi, Tony Hunter, Gene W Yeo

SRA Experiments (4) and Runs (4)

Total: 2731 MB

SRX13634018 SRP353754 RIP-Seq SINGLE

GSM5773932: HEK293_LARP4 eCLIP, rep 1; Homo sapiens; RIP-Seq

Sample: SRS11520760

BioProject: PRJNA795057

BioSample: SAMN24673528

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: HEK293_LARP4 eCLIP

cell line: HEK293

eclip antibody: LARP4 (Bethyl, A303-900A)

molecule: RNA IP

inline barcode1: Ril19

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293_LARP4 eCLIP

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR17462856	21097429	1603404604	663.61	Hek293_WT_P_rep_1_S1_L007_R1_001.fastq.gz, SRR17462856, SRR17462856.l…	SRA

SRX13634019 SRP353754 RIP-Seq SINGLE

GSM5773933: HEK293_LARP4 eCLIP, rep 2; Homo sapiens; RIP-Seq

Sample: SRS11520761

BioProject: PRJNA795057

BioSample: SAMN24673527

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: HEK293_LARP4 eCLIP

cell line: HEK293

eclip antibody: LARP4 (Bethyl, A303-900A)

molecule: RNA IP

inline barcode1: Ril19

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293_LARP4 eCLIP

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR17462855	20227690	1537304440	624.15	Hek293_WT_P_rep_2_S5_L007_R1_001.fastq.gz, SRR17462855, SRR17462855.l…	SRA

SRX13634020 SRP353754 RIP-Seq SINGLE

GSM5773934: HEK293_LARP4 eCLIP, size-matched input, rep 1; Homo sapiens; RIP-Seq

Sample: SRS11520762

BioProject: PRJNA795057

BioSample: SAMN24673526

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: HEK293_LARP4 eCLIP, size-matched input

cell line: HEK293

eclip antibody: none

molecule: RNA size matched input

inline barcode1: Ril19

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293_LARP4 eCLIP, size-matched input

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR17462854	25953479	1972464404	767.13	Hek293_WT_N_rep_1_S9_L007_R1_001.fastq.gz, SRR17462854, SRR17462854.l…	SRA

SRX13634021 SRP353754 RIP-Seq SINGLE

GSM5773935: HEK293_LARP4 eCLIP, size-matched input, rep 2; Homo sapiens; RIP-Seq

Sample: SRS11520763

BioProject: PRJNA795057

BioSample: SAMN24673525

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Homo sapiens

Sample attributes

source_name: HEK293_LARP4 eCLIP, size-matched input

cell line: HEK293

eclip antibody: none

molecule: RNA size matched input

inline barcode1: Ril19

geo_loc_name: missing

collection_date: missing

Original files (1)

HEK293_LARP4 eCLIP, size-matched input

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR17462853	22751223	1729092948	676.42	Hek293_WT_N_rep_2_S13_L007_R1_001.fastq.gz, SRR17462853, SRR17462853.…	SRA

Linked Publications (2)

LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function.

RNA (New York, N.Y.) · 2024

LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function.

RNA (New York, N.Y.) · 2024

Data Files (4)

Accession	File Name	Stored Type	Size	Download
—	Hek293_WT_N_rep_1_S9_L007_R1_001.fastq.gz	RIP-Seq	767.1 MB	link
—	Hek293_WT_N_rep_2_S13_L007_R1_001.fastq.gz	RIP-Seq	676.4 MB	link
—	Hek293_WT_P_rep_1_S1_L007_R1_001.fastq.gz	RIP-Seq	663.6 MB	link
—	Hek293_WT_P_rep_2_S5_L007_R1_001.fastq.gz	RIP-Seq	624.1 MB	link