histone mrnas - OmicsDI

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Organisms

Homo sapiens (65)
Mus musculus (52)
Caenorhabditis elegans (12)
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Drosophila melanogaster (8)
Schizosaccharomyces pombe (7)
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Disease

Lymphoma (1)

Technology Type

Mass Spectrometry (18)
Shotgun proteomics (11)
Affinity purification coupled with mass spectrometry proteomics (5)
Mass spectrometry (2)
Bottom-up proteomics (2)
Illumina HiSeq 2000 (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)
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Gel-based experiment (1)

Instrument Platform

Illumina HiSeq 2000 (2)
Illumina HiSeq 4000 (2)
NextSeq 500 (2)
Liquid Chromatography MS - negative - hilic (2)
Liquid Chromatography MS - positive - hilic (2)
Growth chamber (1)
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Publication Date

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2012 (26)
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2004 (1)

CHEBI ID

CHEBI:125405 (1)
CHEBI:1387 (1)
CHEBI:15318 (1)
CHEBI:15414 (1)
CHEBI:15558 (1)
CHEBI:15603 (1)
CHEBI:15652 (1)
CHEBI:15682 (1)
CHEBI:15741 (1)
CHEBI:15753 (1)
CHEBI:15756 (1)
CHEBI:15843 (1)
CHEBI:16001 (1)
CHEBI:16027 (1)
CHEBI:16142 (1)
CHEBI:16154 (1)
CHEBI:16235 (1)
CHEBI:16264 (1)
CHEBI:16335 (1)
CHEBI:16344 (1)
CHEBI:16349 (1)
CHEBI:16467 (1)
CHEBI:16610 (1)
CHEBI:16675 (1)
CHEBI:1670 (1)
CHEBI:16704 (1)
CHEBI:16708 (1)
CHEBI:16750 (1)
CHEBI:16919 (1)
CHEBI:16927 (1)

Metabolite Name

((4r)-4-((3r,5r,9s,10s,12s,13r,14s,17r)-3,12-dihydroxy-10,13-dimethylhexadecahydro-1h-cyclopenta[a]phenanthren-17-yl)pentanoyl)glycylglycine (1)
(-)-riboflavin (1)
(1e,4e)-1,5-bis(4-methoxyphenyl)penta-1,4-dien-3-one (1)
(2r)-5-methoxy-2-methyl-2,3,8,9-tetrahydrofuro[2,3-h]chromen-4-one (1)
(2r,3s,4s,5r,6r)-5-[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy-2-(hydroxymethyl)-6-(2-phenylethoxy)oxane-3,4-diol (1)
(3as,5r,5as,8as,9ar)-5,8a-dimethyl-1-methylidene-3a,4,5,5a,6,7,9,9a-octahydroazuleno[6,7-b]furan-2,8-dione (1)
(3r,5r,6r,7s,9s,10r,13r,17r)-17-((r)-5-methoxy-5-oxopentan-2-yl)-10,13-dimethylhexadecahydro-1h-cyclopenta[a]phenanthrene-3,6,7-triyl triacetate (1)
(Z)-6-Octadecenoic acid (1)
(r)-(+)-arachidonyl-1'-hydroxy-2'-propylamide (1)
(r)-butyrylcarnitine (1)
(s)-n-(1-amino-1-oxo-3-phenylpropan-2-yl)-1-pentyl-1h-indole-3-carboxamide (1)
(z)-2-octylpent-2-enedioic acid (1)
.alpha.-L-Glu-L-Asp (1)
.alpha.-galactosyl-n-stearoylsphingosine (1)
.beta.-Homoproline (1)
.beta.-d-glucopyranosiduronic acid, 5-[3-[(2,2,3,3-tetramethylcyclopropyl)carbonyl]-1h-indol-1-yl]pentyl (1)
1',4-sophorolactone 6',6-diacetate (1)
1(2h)-pyrimidineacetamide, n-[(1s,3s,4s)-4-[[2-(2,6-dimethylphenoxy)acetyl]amino]-3-hydroxy-5-phenyl-1-(phenylmethyl)pentyl]tetrahydro-4-hydroxy-.alpha.-(1-methylethyl)-2-oxo-, (.alpha.s)- (1)
1,2-diamino-2-methylpropane (1)
1,2-diarachidonoyl-sn-glycero-3-phosphocholine (1)
1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (1)
1,2-dihexadecanoyl-sn-glycerol (1)
1,2-dilinoleoyl-sn-glycero-3-phosphocholine (1)
1,2-dilinoleoyl-sn-glycero-3-phosphoethanolamine (1)
1,2-dilinoleoylglycerol (1)
1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (1)
1,2-dioleoyl-sn-glycero-3-phospho-l-serine (1)
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (1)
1,2-dipalmitoleoyl-sn-glycero-3-phosphoethanolamine (1)
1,2-dipentadecanoyl-sn-glycero-3-phosphocholine (1)

First Public Date

2019 (28)
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2014 (15)
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2016 (7)
2015 (5)
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Classification

protozoa (1)

Study type

Transcription profiling by array (41)
RNA-seq of coding RNA (24)
ChIP-seq (17)
Other (6)
RNA-seq of non coding RNA (6)
ChIP-chip by tiling array (3)
Unknown experiment type (2)
RIP-seq (2)
MicroRNA profiling by high-throughput sequencing (1)
Transcription profiling by tiling array (1)
ChIP-chip by array (1)
CLIP-seq (1)
Transcription profiling by RT-PCR (1)
DNA-seq (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2022 (40)
2015 (39)
2016 (36)
2020 (35)
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2012 (34)
2014 (29)
2017 (28)
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2025 (25)
2019 (25)
2013 (24)
2011 (24)
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2010 (15)
2009 (13)
2008 (9)
2004 (9)
2007 (7)
2026 (5)
2006 (5)
2005 (4)
2002 (3)
2003 (1)
2001 (1)
1999 (1)

Lab affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (2)
EDyP (2)
Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics PAS (2)
3Plateforme Protéomique 3P5-Necker, Structure Fédérative de Recherche Necker and Université Paris Descartes, INSERM US24/CNRS UMS3633, Paris, (1)
Associate Research Professor, Institut de recherches cliniques de Montréal (IRCM) Professeure agrégée, Département de biochimie et médecine moléculaire, Université de Montréal Associate Professor, Division of Experimental Medicine, McGill University (1)
Core facility for mass spectrometry and proteomics ZMBH, University Heidelberg Im Neuenheimer Feld 282 D-69120 Heidelberg (1)
Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA. Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA. (1)
Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (1)
Laboratoire de Spectrometrie de Masse Proteomique Institut Curie PSL Research University (1)
Laboratory of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague 4, 142 20, Czech Republic (1)
MRC Toxicology Unit, University of Cambridge, UK (1)
Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Germany. Bioanalytics, Department of Clinical Chemistry, University Medical Center Goettingen, Germany. (1)
Research Institute of Molecular Pathology (IMP), Austria (1)
University of North Carolina Chapel Hill (1)
Zentrum fuer Molekulare Biologie, University Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany (1)

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Eukaryotic Initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs

In diffuse large B-cell lymphoma (DLBCL) poor outcome is associated with EIF4B-dependent stimulation of the DEAD box helicase eIF4A that unwinds RNA structures in 5’ untranslated regions (UTRs) in mRNAs that encode proteins with a role in cell proliferation. We carried out iCLIP to examine differenc...

ORGANISM(S): Homo sapiens (Human)

2024-09-04 | PXD042538 | Pride

Deep sequencing shows multiple oligouridylations are required for 3' to 5' degradation of histone mRNAs on polyribosomes

We developed a customized RNA-Seq strategy to identify the 3' termini of degradation intermediates of histone mRNAs. Using this strategy, we identified two types of oligouridylated degradation intermediates: RNAs ending at different sites of the 3' side of the stemloop that resulted from initial deg...

ORGANISM(S): Homo sapiens

2014-03-20 | E-GEOD-54922 | biostudies-arrayexpress

Rapid degradation of replication-dependent histone mRNAs largely occurs on mRNAs bound by nuclear cap-binding proteins 80 and 20.

Not available

S-EPMC3553978 | biostudies-literature

Anti-SLBP RIPchip data

The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. They are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in at a conserved stem-loop (SL) structure. This SL structure interacts stably with the...

ORGANISM(S): Homo sapiens

2015-12-16 | E-GEOD-59915 | biostudies-arrayexpress

A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.

Not available

S-EPMC4604434 | biostudies-literature

iCLIP-seq identifies direct binding of PETISCO complex to replication-dependent histone mRNAs in Caenorhabditis elegans embryos

This study uses individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) to map the direct RNA-binding sites of the PETISCO complex in Caenorhabditis elegans embryos. When bound to TOST-1, PETISCO stabilizes replication-dependent histone mRNAs during oogenesis to ensure adequ...

ORGANISM(S): Caenorhabditis elegans

2025-11-11 | E-MTAB-15713 | biostudies-arrayexpress

Protein composition of catalytically active U7-dependent processing complexes assembled on histone pre-mRNA containing biotin and a photo-cleavable linker

To identify components of the U7 snRNP, we used cleavage-resistant histone pre-mRNA containing biotin and a photo-sensitive linker and purify processing complexes from Drosophila and mouse nuclear extracts.

ORGANISM(S): Mus musculus (Mouse) Drosophila melanogaster (Fruit fly)

2018-03-08 | PXD008917 | Pride

Flash lsm11 Histone pre-mrna Photo-cleavable linker 3’ end processing U7 snrnp slbp

ALYREF links 3'processing and nuclear export of histone mRNAs

PRJNA451115 | ENA

A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues.

Not available

S-EPMC5100578 | biostudies-literature

U2 snRNP binds intronless histone pre-mRNAs to facilitate U7-snRNP-dependent 3' end formation.

Not available

S-EPMC2149891 | biostudies-literature

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