GSE135435

GSE GEO

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The Thermus thermophilus DEAD-box protein Hera is a general RNA chaperone and plays a key role in tRNA metabolism

Organism: Thermus thermophilus HB27

Platform: GPL27012

Samples: 8

Experiment Types:

Expression profiling by high throughput sequencing

Submitted: Aug 06 2019

Last Updated: Oct 22 2020

Status: Public on Oct 22 2020

Contact: Gene,,Yeo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA558889 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP217527

Summary

RNA helicases catalyze the ATP-dependent destabilization of RNA duplexes. DEAD-box helicases share a helicase core that mediates ATP binding and hydrolysis, RNA binding and unwinding. Most members of this family contain domains flanking the core that can confer RNA substrate specificity and guide the helicase to a specific RNA. However, the in vivo RNA substrates of most helicase are currently not defined. The DEAD-box helicase Hera from Thermus thermophilus contains a helicase core, followed by a dimerization domain (DD) and an RNA binding domain (RBD) that folds into an RNA recognition motif (RRM). The RRM mediates high affinity binding to an RNA hairpin, and an adjacent duplex is then unwound by the helicase core. Hera is a cold-shock protein, and has been suggested to act as an RNA chaperone under cold-shock conditions. Using immunoprecipitation of Hera-RNA complexes and RNA-Seq, we show that Hera binds to a large fraction of T. thermophilus RNAs under normal-growth and cold-shock conditions without a strong sequence preference, in agreement with a structure-specific recognition of RNAs and a general function in RNA metabolism. Under cold-shock conditions, Hera is recruited to RNAs with high propensities to form stable secondary structures. We show that selected RNAs identified, including a set of tRNAs, bind to Hera in vitro, and activate the Hera helicase core. Gene ontology analysis reveals an enrichment of genes related to translation, including mRNAs of ribosomal proteins, tRNAs, tRNA ligases, and tRNA-modifying enzymes, consistent with a key role of Hera in ribosome assembly and tRNA metabolism.

Overall Design

eCLIP-seq in Thermus thermophilus HB27 (DSM 7039, DSMZ; ATCC BAA-163)

Analysis (29 steps)

View Data Processing

Processing steps for GSE135435

Takes output from raw files.
Run to trim off both 5â and 3â adapters on both reads.
Command: quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.fastq.gz -p /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R1.X1A.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1.
Run to trim off the 3â adapters on read 2, to control for double ligation events.
Command: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz -p /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R2.X1A.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.X1A.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.
Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.

Showing first 8 steps.

Supplementary Files (1)

GSE135435_RAW.tar Download

GEO Samples (8)

GSM4008944 GSM4008945 GSM4008946 GSM4008947 GSM4008948 GSM4008949 GSM4008950 GSM4008951

Dataset Citations (1)

The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.

PMID 32669294 · 2020 · RNA (New York, N.Y.)

Pascal Donsbach, Brian A Yee, Dione Sanchez-Hevia, José Berenguer, Stefan Aigner, Gene W Yeo, Dagmar Klostermeier

SRA Experiments (8) and Runs (8)

Total: 661 MB

SRX6658669 SRP217527 RIP-Seq PAIRED

GSM4008944: eCLIP Thermus thermophilus, normal-growth conditions, replicate 1; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219130

BioProject: PRJNA558889

BioSample: SAMN12501301

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, normal-growth conditions, replicate 1

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

inline barcode1: X1A

inline barcode2: X1B

Original files (1)

eCLIP Thermus thermophilus, normal-growth conditions, replicate 1

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909221	1745927	174592700	67.09	DK_Hera_1_Hera_S59_L004_R1_001.fastq.gz, DK_Hera_1_Hera_S59_L004_R2_0…	SRA

SRX6658670 SRP217527 RIP-Seq PAIRED

GSM4008945: eCLIP Thermus thermophilus, normal-growth conditions, replicate 2; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219131

BioProject: PRJNA558889

BioSample: SAMN12501331

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, normal-growth conditions, replicate 2

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

inline barcode1: X1A

inline barcode2: X1B

Original files (1)

eCLIP Thermus thermophilus, normal-growth conditions, replicate 2

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909222	1456784	145678400	57.8	DK_Hera_2_Hera_S62_L004_R1_001.fastq.gz, DK_Hera_2_Hera_S62_L004_R2_0…	SRA

SRX6658671 SRP217527 RIP-Seq PAIRED

GSM4008946: eCLIP Thermus thermophilus, cold-shock conditions, replicate 1; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219133

BioProject: PRJNA558889

BioSample: SAMN12501330

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, cold-shock conditions, replicate 1

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

inline barcode1: X1A

inline barcode2: X1B

Original files (1)

eCLIP Thermus thermophilus, cold-shock conditions, replicate 1

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909223	1287720	128772000	49.36	DK_Hera_3_Hera_S65_L004_R1_001.fastq.gz, DK_Hera_3_Hera_S65_L004_R2_0…	SRA

SRX6658672 SRP217527 RIP-Seq PAIRED

GSM4008947: eCLIP Thermus thermophilus, cold-shock conditions, replicate 2; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219132

BioProject: PRJNA558889

BioSample: SAMN12501329

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, cold-shock conditions, replicate 2

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

inline barcode1: X1A

inline barcode2: X1B

Original files (1)

eCLIP Thermus thermophilus, cold-shock conditions, replicate 2

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909224	1308176	130817600	51.31	DK_Hera_4_Hera_S40_L003_R1_001.fastq.gz, DK_Hera_4_Hera_S40_L003_R2_0…	SRA

SRX6658673 SRP217527 RIP-Seq PAIRED

GSM4008948: eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 1; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219134

BioProject: PRJNA558889

BioSample: SAMN12501328

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 1

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

Original files (1)

eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 1

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909225	2698144	269814400	104.64	DK_Hera_1_Input_S57_L004_R1_001.fastq.gz, DK_Hera_1_Input_S57_L004_R2…	SRA

SRX6658674 SRP217527 RIP-Seq PAIRED

GSM4008949: eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 2; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219135

BioProject: PRJNA558889

BioSample: SAMN12501327

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 2

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

Original files (1)

eCLIP Thermus thermophilus, normal-growth conditions size-matched input, replicate 2

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909226	2564858	256485800	103.1	DK_Hera_2_Input_S60_L004_R1_001.fastq.gz, DK_Hera_2_Input_S60_L004_R2…	SRA

SRX6658675 SRP217527 RIP-Seq PAIRED

GSM4008950: eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 1; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219136

BioProject: PRJNA558889

BioSample: SAMN12501326

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 1

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

Original files (1)

eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 1

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909227	3300545	330054500	125.67	DK_Hera_3_Input_S63_L004_R1_001.fastq.gz, DK_Hera_3_Input_S63_L004_R2…	SRA

SRX6658676 SRP217527 RIP-Seq PAIRED

GSM4008951: eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 2; Thermus thermophilus HB27; RIP-Seq

Sample: SRS5219137

BioProject: PRJNA558889

BioSample: SAMN12501325

Platform: ILLUMINA

Instrument: Illumina HiSeq 4000

Organism: Thermus thermophilus HB27

Sample attributes

source_name: eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 2

antibody: anti-Hera (rabbit)

antibody manufacturer: Eurogentec

antibody lot: 1335-36

cell line: DSM #7039

Original files (1)

eCLIP Thermus thermophilus, cold-shock conditions size-matched input, replicate 2

Runs (1)

Run	Spots	Bases	Size (MB)	Files	Link
SRR9909228	2565696	256569600	101.98	DK_Hera_4_Input_S38_L003_R1_001.fastq.gz, DK_Hera_4_Input_S38_L003_R2…	SRA

Linked Publications (1)

The <i>Thermus thermophilus</i> DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism.

RNA (New York, N.Y.) · 2020

Data Files (8)

Accession	File Name	Stored Type	Size	Download
—	DK_Hera_1_Hera_S59_L004_R1_001.fastq.gz	RIP-Seq	67.1 MB	link
—	DK_Hera_1_Input_S57_L004_R1_001.fastq.gz	RIP-Seq	104.6 MB	link
—	DK_Hera_2_Hera_S62_L004_R1_001.fastq.gz	RIP-Seq	57.8 MB	link
—	DK_Hera_2_Input_S60_L004_R1_001.fastq.gz	RIP-Seq	103.1 MB	link
—	DK_Hera_3_Hera_S65_L004_R1_001.fastq.gz	RIP-Seq	49.4 MB	link
—	DK_Hera_3_Input_S63_L004_R1_001.fastq.gz	RIP-Seq	125.7 MB	link
—	DK_Hera_4_Hera_S40_L003_R1_001.fastq.gz	RIP-Seq	51.3 MB	link
—	DK_Hera_4_Input_S38_L003_R1_001.fastq.gz	RIP-Seq	102.0 MB	link