scholarly journals Mechanistic constraints on diversity in human V(D)J recombination.

1996 ◽  
Vol 16 (1) ◽  
pp. 258-269 ◽  
Author(s):  
G H Gauss ◽  
M R Lieber
Keyword(s):  
Statistical Analysis ◽  
Base Composition ◽  
Human Cells ◽  
Full Length ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Inverted Repeats ◽  
Stacking Interactions ◽  
Large Collection ◽  
Significant Frequency ◽  
End Sequences

We have analyzed a large collection of coding junctions generated in human cells. From this analysis, we infer the following about nucleotide processing at coding joints in human cells. First, the pattern of nucleotide loss from coding ends is influenced by the base composition of the coding end sequences. AT-rich sequences suffer greater loss than do GC-rich sequences. Second, inverted repeats can occur at ends that have undergone nucleolytic processing. Previously, inverted repeats (P nucleotides) have been noted only at coding ends that have not undergone nucleolytic processing, this observation being the basis for a model in which a hairpin intermediate is formed at the coding ends early in the reaction. Here, inverted repeats at processed coding ends were present at approximately twice the number of junctions as P nucleotide additions. Terminal deoxynucleotidyl transferase (TdT) is required for the appearance of the inverted repeats at processed ends (but not full-length coding ends), yet statistical analysis shows that it is virtually impossible for the inverted repeats to be polymerized by TdT. Third, TdT additions are not random. It has long been noted that TdT has a G utilization preference. In addition to the G preference, we find that TdT adds strings of purines or strings of pyrimidines at a highly significant frequency. This tendency suggests that nucleotide-stacking interactions affect TdT polymerization. All three of these features place constraints on the extent of junctional diversity in human V(D)J recombination.

Litoria gracilenta (Anura : Hylidae) and related species in New Guinea

2004 ◽  
Vol 52 (2) ◽  
pp. 191 ◽  
Author(s):  
J. I. Menzies ◽  
M. J. Tyler
Keyword(s):  
Statistical Analysis ◽  
Related Species ◽  
New Guinea ◽  
Large Collection ◽  
Tree Frogs

We examined a large collection (n = 132) of tree frogs, hitherto identified as Litoria gracilenta, from various localities in New Guinea and compared them with Litoria gracilenta from Queensland and with the recently described Litoria elkeae from far west New Guinea. We found that the frogs in question were neither L. gracilenta nor L. elkeae but comprised two distinct taxa described herein as new species.We call attention to the problems of performing statistical analysis on measurements of soft-bodied organisms and consider that the conclusions reached in this analysis are both conservative and realistic.

scholarly journals DNAskew: Statistical Analysis of Base Compositional Asymmetry and Prediction of Replication Boundaries in the Genome Sequences

2004 ◽  
Vol 36 (1) ◽  
pp. 16-20 ◽  
Author(s):  
Xiang-Ru Ma ◽  
Shao-Bo Xiao ◽  
Ai-Zhen Guo ◽  
Jian-Qiang Lü ◽  
Huan-Chun Chen
Keyword(s):  
Statistical Analysis ◽  
Base Composition ◽  
Script Language ◽  
Genome Sequences ◽  
Strand Asymmetry ◽  
Rule Type ◽  
Codon Composition ◽  
Dna Strands ◽  
Phylogenetic Evolution ◽  
Relationship Of

Abstract Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution, in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

scholarly journals Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells

2021 ◽  
Author(s):  
Evangelos D. Karousis ◽  
Foivos Gypas ◽  
Mihaela Zavolan ◽  
Oliver Muehlemann
Keyword(s):  
Regulation Of Gene Expression ◽  
Degradation Pathway ◽  
Human Cells ◽  
Full Length ◽  
Main Function ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Short Read ◽  
Expression Levels ◽  
Short Read Sequencing

Background: Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge. Results: To identify and analyze endogenous targets of NMD, we applied cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identified, most derive from alternative exon usage. The isoform-aware analysis revealed many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTR per se does not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD still seems to be ridding the transcriptome of isoforms resulting from spurious splicing events. Conclusions: Long-read sequencing enabled the identification of many novel NMD-sensitive mRNAs and revealed both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.

A new approach combining LC-MS and multivariate statistical analysis for revealing changes in histone modification levels

2014 ◽  
Vol 10 (11) ◽  
pp. 2974-2983 ◽  
Author(s):  
Raphaël Bilgraer ◽  
Sylvie Gillet ◽  
Sophie Gil ◽  
Danièle Evain-Brion ◽  
Olivier Laprévote
Keyword(s):  
Statistical Analysis ◽  
Histone Modification ◽  
Multivariate Statistical Analysis ◽  
Histone Code ◽  
Human Cells ◽  
Multivariate Statistical ◽  
New Approach ◽  
Xenobiotic Exposure

We have developed a new global histonomic approach for deciphering histone code disruption in human cells after xenobiotic exposure.

scholarly journals Scalable Production in Human Cells and Biochemical Characterization of Full-Length Normal and Mutant Huntingtin

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0121055 ◽  
Author(s):  
Bin Huang ◽  
Tanja Lucas ◽  
Claudia Kueppers ◽  
Xiaomin Dong ◽  
Maike Krause ◽  
...  
Keyword(s):  
Biochemical Characterization ◽  
Human Cells ◽  
Full Length ◽  
Mutant Huntingtin ◽  
Scalable Production

scholarly journals Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Evangelos D. Karousis ◽  
Foivos Gypas ◽  
Mihaela Zavolan ◽  
Oliver Mühlemann
Keyword(s):  
Regulation Of Gene Expression ◽  
Degradation Pathway ◽  
Human Cells ◽  
Full Length ◽  
Main Function ◽  
Nanopore Sequencing ◽  
Sequencing Data ◽  
Short Read ◽  
Expression Levels ◽  
Short Read Sequencing

Abstract Background Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge. Results To identify and analyze endogenous targets of NMD, we apply cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identifies, most derive from alternative exon usage. The isoform-aware analysis reveals many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTR per se does not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD seems to be ridding the transcriptome of isoforms resulting from spurious splicing events. Conclusions Long-read sequencing enables the identification of many novel NMD-sensitive mRNAs and reveals both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.

Comparative genome analysis suggests characteristics of yeast inverted repeats that are important for transcriptional activity

Genome ◽  
2011 ◽  
Vol 54 (11) ◽  
pp. 934-942 ◽  
Author(s):  
Emily L. Humphrey-Dixon ◽  
Richard Sharp ◽  
Michael Schuckers ◽  
Robin Lock
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genomic Instability ◽  
Genome Analysis ◽  
Base Composition ◽  
Transcriptional Activity ◽  
Dna Structure ◽  
Inverted Repeats ◽  
Comparative Genome Analysis ◽  
Comparative Genome

Inverted repeats are sequences of DNA that, when read in the 5′ to 3′ direction, have the same sequence on both strands (palindromic portion), with the exception of a small number of nucleotides in the exact center (nonpalindromic spacer). They have been implicated in various DNA-mediated processes including replication, transcription, and genomic instability. At least some of these sequences are capable of forming an alternative DNA structure, called a cruciform, that may be important for mediating these functions. We generated a list of inverted repeats in the Saccharomyces cerevisiae genome and determined which of them are conserved in three related yeasts. We have identified characterisitics of inverted repeats that make them more likely to be conserved than the surrounding DNA and characteristics, such as position and base composition, that make the genes they are associated with likely to be more actively transcribed. This is an important step in determining the functions of this group of genomic elements.

scholarly journals Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer

2019 ◽  
Vol 295 (4) ◽  
pp. 1105-1119 ◽  
Author(s):  
Mukul Sherekar ◽  
Sae-Won Han ◽  
Rodolfo Ghirlando ◽  
Simon Messing ◽  
Matthew Drew ◽  
...  
Keyword(s):  
Tumor Suppressor ◽  
Analytical Ultracentrifugation ◽  
Small Gtpases ◽  
Human Cells ◽  
Full Length ◽  
Mitogen Activated Protein Kinase ◽  
Size Exclusion ◽  
Type I ◽  
High Affinity

Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS–mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography–multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro. The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.

Deoxyribonucleic acid base composition of isolates of Rhizobium japonicum

1969 ◽  
Vol 15 (5) ◽  
pp. 490-493 ◽  
Author(s):  
Gerald H. Elkan
Keyword(s):  
Statistical Analysis ◽  
Base Composition ◽  
Deoxyribonucleic Acid ◽  
Genetic Relatedness ◽  
The Other ◽  
Rhizobium Japonicum ◽  
Acid Base ◽  
Dna Base Composition ◽  
Dna Base ◽  
Mole Percentage

The DNA base composition (expressed as mean molar percentages of guanine and cytosine) of 25 strains of Rhizobium japonicum was determined to study the genetic relatedness of these strains. The mole percentage GC ranged from 61.47 to 64.09. Statistical analysis of the DNA base ratios of the 25 isolates revealed that 16 of these differed significantly in GC ratios from some of the other strains.

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