Periodicities of 10–11 bp as Indicators of the Supercoiled State of Genomic DNA

Schieg, Patrick; Herzel, Hanspeter

doi:10.1016/j.jmb.2004.08.068

Cited by 43 publications

(53 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our results confirm a bimodal distribution of predominant periodicities among prokaryotes previously observed by Herzel and coworkers and ascribed to different supercoiling propensities (13,14,34). However, the larger collection of analyzed genomes and analysis of intrachromosomal heterogeneity of the periodic signal performed in this study provide a more nuanced picture.…”

Section: Discussionsupporting

confidence: 91%

“…Figure 3 and Table S1 in the supplemental material show the MaxQ and PMaxQ indices for all 1,025 chromosomes analyzed with the A2T2 method (dinucleotides AA/TT) and spacing range 30 to 100 bp. Consistent with earlier work (14,27,34), most bacteria have PMaxQ around 11 bp or slightly higher whereas many archaea have PMaxQ near 10 bp. For genomes analyzed previously by Schieg and Herzel (34), the PMaxQ rarely differs by more than 0.1 bp from their "fitting period" (see Table S1 in the supplemental material).…”

Section: ͔͒supporting

confidence: 90%

“…S5 in the supplemental material). The shift in the predominant period is consistent with the previously reported distinction between bacteria and archaea (14,34). We define aperiodic segments as those with Q*(P) of Ͻ1.5 in the range 10.4 Յ P Յ 11.4.…”

supporting

confidence: 85%

“…These tools were subsequently employed to com-pare properties of periodic signals among 1,025 available complete prokaryotic chromosomes. Our analysis differs from the earlier work (13,14,34,38) not only by using a larger data set of available complete genomes but also by including assessments of intrachromosomal heterogeneity of the periodic signal. This leads to new results that require modifications of previously proposed models for the role of sequence periodicity and intrinsic DNA curvature in prokaryotes.…”

mentioning

confidence: 99%

“…Herzel and coworkers (13,14,34) noted distinct periodic patterns in archaea and bacteria, with periods close to 10 bp being most common in archaea and periods close to 11 bp prevalent in bacteria. They attributed the difference to possible distinct supercoiling propensities of bacterial and archaeal DNA: the periods shorter than the average DNA helical period of ϳ10.5 bp lead to formation of left-handed superhelices corresponding to positive supercoiling, whereas periods larger than 10.5 bp promote right-handed superhelices and negative supercoiling.…”

mentioning

confidence: 99%

See 4 more Smart Citations

Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression

Mrázek

2010

J Bacteriol

View full text Add to dashboard Cite

Regular spacing of short runs of A or T nucleotides in DNA sequences with a period close to the helical period of the DNA double helix has been associated with intrinsic DNA bending and nucleosome positioning in eukaryotes. Analogous periodic signals were also observed in prokaryotic genomes. While the exact role of this periodicity in prokaryotes is not known, it has been proposed to facilitate the DNA packaging in the prokaryotic nucleoid and/or to promote negative or positive supercoiling. We developed a methodology for assessments of intragenomic heterogeneity of these periodic patterns and applied it in analysis of 1,025 prokaryotic chromosomes. This technique allows more detailed analysis of sequence periodicity than previous methods where sequence periodicity was assessed in an integral form across the whole chromosome. We found that most genomes have the periodic signal confined to several chromosomal segments while most of the chromosome lacks a strong sequence periodicity. Moreover, there are significant differences among different prokaryotes in both the intensity and persistency of sequence periodicity related to DNA curvature. We proffer that the prokaryotic nucleoid consists of relatively rigid sections stabilized by short intrinsically bent DNA segments and characterized by locally strong periodic patterns alternating with regions featuring a weak periodic signal, which presumably permits higher structural flexibility. This model applies to most bacteria and archaea. In genomes with an exceptionally persistent periodic signal, highly expressed genes tend to concentrate in aperiodic sections, suggesting that structural heterogeneity of the nucleoid is related to local differences in transcriptional activity.DNA sequences generally contain two strong periodic signals. The dominant signal has a period of 3 bp and relates to biased codon and amino acid usages in protein-coding genes. The second significant periodic signal has a period close to 10.5 bp (the average length of a helical turn of DNA in the canonical B conformation) and relates to DNA curvature and/or bendability. This periodic signal is most pronounced in the distribution of short runs of A or T (37,39,40). In eukaryotes, the DNA periodicity is a primary nucleosome positioning signal-the intrinsically bent DNA both facilitates wrapping of the DNA around the histone core and restricts the placement of nucleosomes (22,35,36,40). The periodic pattern in the DNA sequence can influence characteristics of the chromatin and consequently the molecular interactions associated with transcription. In particular, patterns of sequence periodicity in the Caenorhabditis elegans genome are related to histone modifications, and regions with strong periodic signals are associated with germ line-specific genes, suggesting that periodicity within chromosomal segments can affect levels of gene expression (9,12,17).Previous analyses of periodic signals in prokaryotic DNA sequences raised interesting questions about possible roles the sequence periodicity and c...

show abstract

Section: Discussionsupporting

confidence: 91%

Section: ͔͒supporting

confidence: 90%

supporting

confidence: 85%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression

Mrázek

2010

J Bacteriol

View full text Add to dashboard Cite

show abstract

Analysis of nucleoid‐associated protein‐binding regions reveals DNA structural features influencing genome organization in Mycobacterium tuberculosis

et al. 2021

View full text Add to dashboard Cite

Nucleoid‐associated proteins (NAPs) maintain bacterial nucleoid configuration through their architectural properties of DNA bending, wrapping, and bridging. However, the contribution of DNA structural alterations to DNA‐NAP recognition at the genomic scale remains unresolved. Present work dissects the DNA sequence, shape and altered structural preferences at a genomic scale for six NAPs in Mycobacterium tuberculosis. Results suggest narrower minor groove width (MGW) and higher DNA rigidity are marked for the binding sites of EspR and Lsr2, while mIHF, MtHU and NapM have heterogeneous DNA structural predilections. In contrast, WhiB4–DNA‐binding sites were characterized by wider MGW, highly deformable and less curved DNA. This work provides systematic insight into NAP‐mediated genome organization as a function of DNA structural features.

show abstract

References

2006

Archaea

View full text Add to dashboard Cite

Periodicities of 10–11 bp as Indicators of the Supercoiled State of Genomic DNA

Cited by 43 publications

References 36 publications

Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression

Comparative Analysis of Sequence Periodicity among Prokaryotic Genomes Points to Differences in Nucleoid Structure and a Relationship to Gene Expression

Analysis of nucleoid‐associated protein‐binding regions reveals DNA structural features influencing genome organization in Mycobacterium tuberculosis

References

Contact Info

Product

Resources

About