BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1511170000?filename=MODEL1511170000_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1511170000?filename=MODEL1511170000_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1511170000?filename=MODEL1511170000.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL1511170000?filename=MODEL1511170000.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1511170000?filename=MODEL1511170000.vcmlprimaryOK200Veronica Llorens-RicoNon-curatedordinary differential equation modelL2V4https://www.ebi.ac.uk/biomodels/MODEL151117000026973873falseBioModelsSBMLModelsLlorénsRico2016 Effects of cis Encoded antisense RNAs (asRNAs) Case12016MODEL1511170000Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano L, Lluch-Senar MLloréns-Rico V26973873,
cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing nine different asRNAs in Mycoplasma pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.. null, 2.
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.veronica.llorens@crg.euCentre for Genomic Regulation, CRGcis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing nine different asRNAs in Mycoplasma pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.Bacterial antisense RNAs are mainly the product of transcriptional noise.Lloréns-Rico Verónica V, Cano Jaime J, Kamminga Tjerko T, Gil Rosario R, Latorre Amparo A, Chen Wei-Hua WH, Bork Peer P, Glass John I JI, Serrano Luis L, Lluch-Senar Maria Mcarcinoma in situ, BB234005, ahl4, BACTS2., CIS-1, SOCS, CIS, Cis, malignant, in situ, G18, Protein G18, carcinoma, 9030605P22Rik, epithelial tumor, intraepithelial carcinoma, stage 0 disease, Suppressor of cytokine signaling, non-invasive carcinoma, 2610511A05Rikextent, Ghrfr, transcription, Transcriptome Profile, number, Gene Expression Profile, Gene, Profiles, eubacteria, 2610511A05Rik, composed of, Ximpact, BB234005, Roles, Concepts, Low, Genomes., me75, Eubacteria, Profile, messenger RNA, composition, number of, non-invasive carcinoma, Signatures, D17Mit170, Monera, T1, Chloroplast, Etioplast, DNA-dependent, template RNA, Bacteria <bacteria>, Expression Signature, Prokaryotae, in situ, Role Concepts, has or lacks parts of type, Transcriptomes, Protein G18, carcinoma, species, fungi, Procaryotae, transcription from bacterial-type RNA polymerase promoter, BACTS2, carcinoma in situ, ahl4, cellular transcription, bacteria, Noise, Transcriptome, cou, DNA-dependent transcription, completeness, malignant, Expression Profiles, Pollution, lit, extra or missing physical or functional parts, Etioplasts, compositionality, Tl3, Tl2, INSDC_feature:misc_RNA, impact-a, results, Concept, mereological quality, Gene Expression, Lr, Role Concept, CIS, Cis, Expression Signatures, Gene Expression Signatures, G18, Role, INSDC_feature:mRNA, prokaryotes, Gene Expression Signature, intraepithelial carcinoma, Expression Profile, Transcriptome Profiles, little, CIS-1, protein_coding_transcript, mRNA, content, DNA-templated, 9030605P22Rik, stage 0 disease, Noises, SOCS, Gene Expression Profiles, prokaryote, bacterial transcription, cardinality, structure, Bra, Noise Pollution, Eaton Agent, epithelial tumor, Signature, Suppressor of cytokine signaling, E430016J11Rik, RWDD5, Prokaryotaextent, multicellular organismal catabolic process, single-organism catabolic process, Forms, protein translation, transcription, Sectors, Public Sectors, Meth, number, ribosomal RNA, Copyrights, eubacteria, monosomy 2q32, 2610511A05Rik, Chalk, composed of, Ximpact, presence, BB234005, SATB2 syndrome, glass syndrome, Roles, Tina, Concepts, Low, Public Enterprise, monosomy 2q32q33, Enterprises, MAR, study, me75, Eubacteria, Glass, Genomes, catabolism, ligand, Public Domains, messenger RNA, composition, number of, non-invasive carcinoma, Public Enterprises, D17Mit170, Monera, T1, Chloroplast, Etioplast, DNA-dependent, template RNA, chromosome 2q32-q33 deletion syndrome, Abstract, Bacteria <bacteria>, Ice, Prokaryotae, in situ, Role Concepts, has or lacks parts of type, Protein G18, monosomy 2q32-q33, carcinoma, species, fungi, Procaryotae, Enterprise, transcription from bacterial-type RNA polymerase promoter, BACTS2, carcinoma in situ, ahl4, 2q32-q33 microdeletion syndrome, protein anabolism, cellular transcription, bacteria, Noise, protein biosynthetic process, cou, degradation, 2q32q33 microdeletion syndromes, IRF-1, DNA-dependent transcription, completeness, malignant, Pollution, extra or missing physical or functional parts, Etioplasts, compositionality, Tl3, Tl2, INSDC_feature:misc_RNA, impact-a, results, Concept, mereological quality, glass, count in organism, Lr, Role Concept, Public, Public Domain, CIS, Cis, SATB2-associated syndrome, G18, protein formation, Del(2)(q32), Role, Domains, INSDC_feature:mRNA, protein biosynthesis, prokaryotes, intraepithelial carcinoma, membrane bound ribosome, Domain, Data Base, free ribosome, Crystal, CIS-1, Ribosome, SAS, 2q32q33 microdeletion syndrome, breakdown, protein_coding_transcript, mRNA, content, DNA-templated, 9030605P22Rik, Del(2)(q32q33), stage 0 disease, Noises, Speed, Sector, protein synthesis, SOCS, prokaryote, bacterial transcription, cardinality, structure, Bra, Public., Noise Pollution, Eaton Agent, epithelial tumor, quantitative, Suppressor of cytokine signaling, E430016J11Rik, RWDD5, Prokaryota, presence or absence in organismPollution, Noise Pollution, Noise, Noises.falseLlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1
LlorénsRico2016 - Effects of cis-Encoded antisense RNAs (asRNAs) - Case1
Three
putative effects of the asRNAs were considered in this study: in
case 1
(this
model)
,
the binding of the asRNA to the corresponding mRNA induces
degradation of the duplex. In case 2, the binding of the asRNA to
the mRNA induces degradation of the mRNA, but not of the asRNA.
In case 3, the mRNA and the asRNA bind reversibly to form a
stable duplex, preventing translation of the mRNA. In all the
three cases, binding to the ribosome protects the mRNA from the
effect of the asRNA.
This model is described in the article:
Bacterial antisense RNAs are
mainly the product of transcriptional noise.
Lloréns-Rico V, Cano J,
Kamminga T, Gil R, Latorre A, Chen WH, Bork P, Glass JI, Serrano
L, Lluch-Senar M.
Sci Adv 2016 Mar; 2(3): e1501363
Abstract:
cis-Encoded antisense RNAs (asRNAs) are widespread along
bacterial transcriptomes. However, the role of most of these
RNAs remains unknown, and there is an ongoing discussion as to
what extent these transcripts are the result of transcriptional
noise. We show, by comparative transcriptomics of 20 bacterial
species and one chloroplast, that the number of asRNAs is
exponentially dependent on the genomic AT content and that
expression of asRNA at low levels exerts little impact in terms
of energy consumption. A transcription model simulating mRNA
and asRNA production indicates that the asRNA regulatory effect
is only observed above certain expression thresholds,
substantially higher than physiological transcript levels.
These predictions were verified experimentally by
overexpressing nine different asRNAs in Mycoplasma pneumoniae.
Our results suggest that most of the antisense transcripts
found in bacteria are the consequence of transcriptional noise,
arising at spurious promoters throughout the genome.
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2017-05-032017-05-182015-11-17MODEL151117000026973873MODEL1511170000