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On diverse biophysical aspects of genetics: from the action of regulators to the characterization of transcripts
KTH, School of Computer Science and Communication (CSC), Computational Biology, CB.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Genetics is among the most rewarding fields of biology for the theoretically inclined, offering both room and need for modeling approaches in the light of an abundance of experimental data of different kinds. Many aspects of the field are today understood in terms of physical and chemical models, joined by information theoretical descriptions. This thesis discusses different mechanisms and phenomena related to genetics, employing tools from statistical physics along with experimental biomolecular methods. Five articles support this work.

Two articles deal with interactions between proteins and DNA. The first one reports on the properties of non-specific binding of transcription factors proteins in the yeast Saccharomyces cerevisiae, due to an effective background free energy which describes the affinity of a single protein for random locations on DNA. We argue that a background pool of non-specific binding sites is filled up before specific binding sites can be occupied with high probability, thus presenting a natural filter for genetic responses to spurious transcription factor productions. The second article describes an algorithm for the inference of transcription factor binding sites for proteins using a realistic physical model. The functionality of the method is verified on a set of known binding sequences for Escherichia coli transcription factors.

The third article describes a possible genetic feedback mechanism between human cells and the ubiquitous Epstein-Barr virus (EBV). 40 binding regions for the major EBV transcription factor EBNA1 are identified in human DNA. Several of these are located nearby genes of particular relevance in the context of EBV infection and the most interesting ones are discussed.

The fourth article describes results obtained from a positional autocorrelation analysis of the human genome, a simple technique to visualize and classify sequence repeats, constituting large parts of eukaryotic genomes. Applying this analysis to genome sequences in which previously known repeats have been removed gives rise to signals corroborating the existence of yet unclassified repeats of surprisingly long periods.

The fifth article combines computational predictions with a novel molecular biological method based on the rapid amplification of cDNA ends (RACE), coined 5’tagRACE. The first search for non-coding RNAs encoded in the genome of the opportunistic bacterium Enterococcus faecalis is performed here. Applying 5’tagRACE allows us to discover and map 29 novel ncRNAs, 10 putative novelm RNAs and 16 antisense transcriptional organizations.

Further studies, which are not included as articles, on the monitoring of secondary structure formation of nucleic acids during thermal renaturation and the inference of genetic couplings of various kinds from massive gene expression data and computational predictions, are outlined in the central chapters.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology , 2011. , xxii, 98 p.
Series
Trita-CSC-A, ISSN 1653-5723 ; 2011:04
Keyword [en]
transcription regulation, regulatory motifs, binding affinity, genetic interactions, secondary structure, sequence repeats, transcript characterization
National Category
Condensed Matter Physics
Identifiers
URN: urn:nbn:se:kth:diva-31490ISBN: 978-91-7415-911-0OAI: oai:DiVA.org:kth-31490DiVA: diva2:404329
Public defence
2011-04-06, Sal FB53, Roslagstullsbacken 21, AlbaNova, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
QC 20110316Available from: 2011-03-17 Created: 2011-03-16 Last updated: 2011-03-17Bibliographically approved
List of papers
1. Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae
Open this publication in new window or tab >>Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae
2007 (English)In: Physical Biology, ISSN 1478-3975, Vol. 4, no 2, 134-143 p.Article in journal (Refereed) Published
Abstract [en]

Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics, and the binding to functional sites must be controlled with a certain specificity for living organisms to be able to elicit specific cellular responses. Specificity stems here from the interplay between binding affinity and cellular abundance of transcription factor proteins, and the binding of such proteins to DNA is thus controlled by their chemical potential. We combine large-scale protein abundance data in the budding yeast with binding affinities for all transcription factors with known DNA binding site sequences to assess the behavior of their chemical potentials in an exponential growth phase. A sizable fraction of transcription factors is apparently bound non-specifically to DNA, and the observed abundances are marginally sufficient to ensure high occupations of the functional sites. We argue that a biological cause of this feature is related to its noise-filtering consequences: abundances below physiological levels do not yield significant binding of functional targets and mis-expressions of regulated genes may thus be tamed.

Keyword
FACILITATED TARGET LOCATION, GENE-REGULATION, NETWORK MOTIFS, REGULATORY NETWORK, ESCHERICHIA-COLI, DNA INTERACTION, SINGLE-CELL, PROTEIN, EXPRESSION, NUMBERS
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-7972 (URN)10.1088/1478-3975/4/2/006 (DOI)000247779500007 ()2-s2.0-34447279073 (ScopusID)
Note
QC 20101005. Tidigare titel:"Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae. Numbers and affinity".Available from: 2008-02-12 Created: 2008-02-12 Last updated: 2011-03-17Bibliographically approved
2. QPS - quadratic programming sampler: a motif finder using biophysical modeling
Open this publication in new window or tab >>QPS - quadratic programming sampler: a motif finder using biophysical modeling
2008 (English)Article in journal (Other academic) Submitted
Abstract [en]

We present a Markov chain Monte Carlo algorithm for local alignments of nucleotide sequences aiming to infer putative transcription factor binding sites, referred to as the quadratic programming sampler. The new motif nder incorporates detailed biophysical modeling of the transcription factor binding site recognition which arises an intrinsic threshold discriminating putative binding sites from other/background sequences.

We validate the principal functioning of the algorithm on a sample of four promoter regions from Escherichia coli. The resulting description of the motif can be readily evaluated on the whole genome to identify new putative binding sites.

Keyword
Transcription Factor Protein, Binding Site Inference, Energy Matrix, MCMC
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-7973 (URN)
Note
QS 20120314Available from: 2008-02-12 Created: 2008-02-12 Last updated: 2012-03-14Bibliographically approved
3. FR-like EBNA1 binding repeats in the human genome
Open this publication in new window or tab >>FR-like EBNA1 binding repeats in the human genome
2010 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 405, no 2, 524-529 p.Article in journal (Refereed) Published
Abstract [en]

Epstein Barr Virus (EBV) is widely spread in the human population. EBV nuclear antigen 1 (EBNA1) is a transcription factor that activates viral genes and is necessary for viral replication and partitioning, which binds the EBV genome cooperatively. We identify similar EBNA1 repeat binding sites in the human genome using a nearest-neighbour positional weight matrix. Previously experimentally verified EBNA1 sites in the human genome are successfully recovered by our approach. Most importantly, 40 novel regions are identified in the human genome, constituted of tandemly repeated binding sites for EBNA1. Genes located in vicinity of these regions are presented as possible targets for EBNA1-mediated regulation. Among these, four are discussed in more detail: IQCB1, IMPG1, IRF2BP and TPO. Incorporating the cooperative actions of EBNA1 is essential when identifying regulatory regions in the human genome and we believe the findings presented here are highly valuable for the understanding of EBV-induced phenotypic changes.

Keyword
EBNA1, Epstein-Barr virus, Family of Repeats, Human binding sites
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:kth:diva-12093 (URN)10.1016/j.virol.2010.06.040 (DOI)000281130500028 ()20655080 (PubMedID)2-s2.0-77955661979 (ScopusID)
Note
QC 20100720. Updated from submitted to published 20120326Available from: 2010-03-03 Created: 2010-03-03 Last updated: 2012-03-26Bibliographically approved
4. Autocorrelation maps of masked sequences reveal novel repeats
Open this publication in new window or tab >>Autocorrelation maps of masked sequences reveal novel repeats
(English)Manuscript (preprint) (Other academic)
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-31474 (URN)
Note
QC 20110316Available from: 2011-03-16 Created: 2011-03-16 Last updated: 2011-03-17Bibliographically approved
5. A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis
Open this publication in new window or tab >>A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis
Show others...
2011 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 39, no 7, E46- p.Article in journal (Refereed) Published
Abstract [en]

Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5'RACE-derivative method coined '5'tagRACE', to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5'tagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5'tagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxin-antitoxin modules.

Keyword
antitoxin, bacterial RNA, messenger RNA, RNA polymerase, TxpA toxin, unclassified drug, untranslated RNA
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:kth:diva-31483 (URN)10.1093/nar/gkr012 (DOI)000289628400006 ()21266481 (PubMedID)2-s2.0-79954609527 (ScopusID)
Funder
Swedish Research Council, 2006-156
Note
QC 20110316Available from: 2011-03-16 Created: 2011-03-16 Last updated: 2012-08-22Bibliographically approved

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