dc.contributor.advisor | Bohnsack, Markus Prof. Dr. | |
dc.contributor.author | Kretschmer, Jens | |
dc.date.accessioned | 2018-04-13T08:07:14Z | |
dc.date.available | 2018-04-13T08:07:14Z | |
dc.date.issued | 2018-04-13 | |
dc.identifier.uri | http://hdl.handle.net/11858/00-1735-0000-002E-E3B9-B | |
dc.identifier.uri | http://dx.doi.org/10.53846/goediss-6829 | |
dc.language.iso | eng | de |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | |
dc.subject.ddc | 572 | de |
dc.title | Interactions and functions of RNA-binding proteins | de |
dc.type | doctoralThesis | de |
dc.contributor.referee | Rehling, Peter Prof. Dr. | |
dc.date.examination | 2017-01-20 | |
dc.description.abstracteng | Alongside several well-known modifications in DNA and proteins, more than 100 different
types of chemical modification are also found in cellular RNAs. RNA modifications can
influence the secondary structure and interactions of the RNAs that carry them and they
can therefore play important roles in regulating the functions of the RNAs. For many RNA
modifications, the enzymes that introduce them are known but the modification targets of
several predicted modification enzymes remain to be identified. Interestingly, a particular
modification, N6-methyladenosine (m6A), was recently found to be reversible and a group
of proteins, termed “readers” that can recognise the modification often via a specialised
RNA binding domain (YTH domain), have been identified. Such “reader” proteins have
been shown to regulate the fate of RNAs according to their modification status,
suggesting that this so called “epitranscriptome” is an additional layer of regulation of
gene expression.
In this study, cross-linking and analysis of cDNA (CRAC) was used to identify the RNAinteractome
of the five human YTH domain-containing proteins, YTHDF1, YTHDF2,
YTHDF3, YTHDC1, YTHDC2. To facilitate the mapping of the deep sequencing data
obtained from CRAC experiments performed in human cells, a bioinformatic pipeline was
adapted and further developed. Analysis of the CRAC data showed that YTHDF1,
YTHDF2, YTHDF3 and YTHDC1 predominantly cross-link to mRNAs, which is in line
with recently published reports describing functions for these proteins in mRNA
degradation, alternative pre-mRNA splicing and enhancing mRNA translation.
Interestingly, the CRAC analysis of YTHDC2 revealed a specific cross-linking site on the
18S ribosomal RNA and the association of this protein with ribosomal complexes was
confirmed by independent experimental approaches. CRAC analysis using truncated
versions of YTHDC2 suggested that the R3H RNA binding domain is required for stable
association of this protein with the ribosome and in vitro anisotropy experiments
demonstrated that the YTH domain of YTHDC2 has a higher affinity for m6A
modifications present in the sequence context found in the ribosomal RNAs than the
classical m6A consensus motif found in many mRNAs. Interestingly, immunoprecipitation
experiments followed by mass spectrometry identified the cytoplasmic 5’-3’ exonuclease
XRN1 as an interaction partner of YTHDC2. These data could suggest a model in which
recognition of the m6A modification(s) on the ribosomal RNA by the YTH domain of
YTHDC2 promotes RNA degradation by XRN1. Taken together, this study contributes to
the understanding of the diverse functions that modification “reader” proteins can play in
regulating RNA metabolism. | de |
dc.contributor.coReferee | Neumann, Heinz Prof. Dr. | |
dc.contributor.thirdReferee | Höbartner, Claudia Prof. Dr. | |
dc.contributor.thirdReferee | Ficner, Ralf Prof. Dr. | |
dc.contributor.thirdReferee | Stülke, Jörg Prof. Dr. | |
dc.subject.eng | RNA biology | de |
dc.subject.eng | RNA modification | de |
dc.subject.eng | ribosome | de |
dc.identifier.urn | urn:nbn:de:gbv:7-11858/00-1735-0000-002E-E3B9-B-8 | |
dc.affiliation.institute | Göttinger Graduiertenschule für Neurowissenschaften, Biophysik und molekulare Biowissenschaften (GGNB) | de |
dc.subject.gokfull | Biologie (PPN619462639) | de |
dc.identifier.ppn | 1018642080 | |