9 research outputs found
Human mutation/substitution rate: Variability, modeling and applications
No full textMutation generates genetic variation, and in turn selection purges deleterious variants from the population. Understanding both is critical for discovering causal genes and variants behind diseases or making inferences about evolutionary processes. Human mutation rate varies significantly across the genome although most studies have only considered the immediate flanking nucleotides around the polymorphic site to model and study patterns of variability. The impact of larger sequence context has not been fully clarified, even though it substantially influences rates of mutation. In the first part of this thesis, I develop a novel statistical framework and using data from the 1000 Genomes project, demonstrate that a larger heptanucleotide sequence context explains \u3e81% variability in substitution probabilities, discovering novel mutation promoting motifs at ApT dinucleotides, CAAT, and TACG sequences. My approach also reveals previously undocumented variability in C-to-T substitutions at CpG sites, not immediately explained by differential methylation intensity. Building on this framework, I model the selective forces acting on the coding genome and develop statistical scores that measures the intolerance at the gene or amino-acid level for functional variants. I demonstrate clinical utility of such intolerance scores in identifying genes associated with multiple human diseases including Autism. Next, I apply these lessons of mutation rate variability to develop an algorithm to detect sub-genic enrichment of de novo germline mutations in RB1 gene of bilateral Retinoblastoma (RB) probands to further elucidate disease biology. I demonstrate that previously noted ‘hotspots’ of nonsense mutations in RB1 are compatible with the elevated mutation rates expected at CpG sites, refuting a specific mechanism in RB pathogenesis. I also find enrichment of splice-site donor mutations of exon 6 and 12 but depletion at exon 5, indicative of previously unappreciated heterogeneity in penetrance within this class of substitution. Finally, I generate more accurate and informative estimates of de novo germline mutation rate in humans, and develop a toolkit to simulate, distribute and interpret mutations in human diseases. Overall, my research uncovers novel variability in human mutation rate and provides a systematic framework for analyzing mutational data, which can be used from causal gene discovery to elucidating specific disease mechanisms
An expanded sequence context model broadly explains variability in polymorphism levels across the human genome
No full text
Viral communities of the human gut: metagenomic analysis of composition and dynamics
No full textAbstract Background The numerically most abundant biological entities on Earth are viruses. Vast populations prey on the cellular microbiota in all habitats, including the human gut. Main body Here we review approaches for studying the human virome, and some recent results on movement of viral sequences between bacterial cells and eukaryotic hosts. We first overview biochemical and bioinformatic methods, emphasizing that specific choices in the methods used can have strong effects on the results obtained. We then review studies characterizing the virome of the healthy human gut, which reveal that most of the viruses detected are typically uncharacterized phage - the viral dark matter - and that viruses that infect human cells are encountered only rarely. We then review movement of phage between bacterial cells during antibiotic treatment. Here a radical proposal for extensive movement of antibiotic genes on phage has been challenged by a careful reanalysis of the metagenomic annotation methods used. We then review two recent studies of movement of whole phage communities between human individuals during fecal microbial transplantation, which emphasize the possible role of lysogeny in dispersal. Short conclusion Methods for studying the human gut virome are improving, yielding interesting data on movement of phage genes between cells and mammalian host organisms. However, viral populations are vast, and studies of their composition and function are just beginning
Additional file 3: Figure S2. of De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm
No full textDonor splice mutations in Exons 5, 6 and 12, and their effect on codon structure. The codon structures are shown prior and after the donor splice mutation. The donor splice mutation results in exon skipping or deletion, but can also cause a frameshift mutation in certain cases. (PDF 84Â kb
Additional file 1: Table S1. of De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm
No full textAll de novo germline variants in RB1 gene of patients with RB. “gDNA position” is the nucleotide position in the GENBANK accession number L11910 of the gene. Table S2. All ExAC variants in RB1 gene that were considered in our analysis. “gDNA position” is the nucleotide position in the GENBANK accession number L11910 of the gene. Table S3. All Nonsense variants in RB1 gene from Onadim and Houdayer groups. “gDNA position” is the nucleotide position in the GENBANK accession number L11910 of the gene. Table S4. Comparison of observed mutations and the simulated frequency of nonsense changes per exon, to find differential pathogenicity within nonsense mutations. Analysis was performed on data from Onadim and Houdayer groups. Table S5. Comparison of observed mutations and the simulated frequency of nonsense changes to find differential pathogenicity within nonsense mutations. Data shown for all amino acids and two arginine codons (99% CI) which can change to a stop codon. Analysis was performed on data from Onadim and Houdayer groups. Table S6. Polyphen predictions on the de novo germline missense mutations or some potential variants near codon 661 in RB1 gene. “Polyphen2_format” is the variant format accepted by the Polyphen2 tool. “Polyphen_prediction” is the result of Polyphen2 on the missense variant. Table S7. Comparison between observed mutations and the simulated frequency of missense changes at amino acids and codons in exon 20, to find localized pathogenicity within missense mutations. Only the significant results are reported here. Table S8. Genomic territory of RB1 gene analyzed in our study. “Position Start” is the start position of the entry as per GENBANK database. “Position End” is the end positon of the entry as per GENBANK database. “Annotation” is the description of the entry. Possible keywords are exon or donor/acceptor region in essential splice or nonessential intronic region. “Exon” corresponds to exon number of the entry. (XLSX 30 kb
Additional file 2: Figure S1. of De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm
No full textComparison of observed mutations and the simulated frequency of essential splice acceptor mutations in RB (99% CI) to find exon specific differential pathogenicity within essential splice mutations. Exons where the observed mutations are higher or lower than the 99% confidence interval of simulations are denoted by an asterisk (*). (PDF 143Â kb
Lamin B1 Depletion in Senescent Cells Triggers Large-Scale Changes in Gene Expression and the Chromatin Landscape
No full textSenescence is a stable proliferation arrest, associated with an altered secretory pathway, thought to promote tumor suppression and tissue aging. While chromatin regulation and lamin B1 down-regulation have been implicated as senescence effectors, functional interactions between them are poorly understood. We compared genome-wide Lys4 trimethylation on histone H3 (H3K4me3) and H3K27me3 distributions between proliferating and senescent human cells and found dramatic differences in senescence, including large-scale domains of H3K4me3- and H3K27me3-enriched “mesas” and H3K27me3-depleted “canyons.” Mesas form at lamin B1-associated domains (LADs) in replicative senescence and oncogene-induced senescence and overlap DNA hypomethylation regions in cancer, suggesting that pre-malignant senescent chromatin changes foreshadow epigenetic cancer changes. Hutchinson-Gilford progeria syndrome fibroblasts (mutant lamin A) also show evidence of H3K4me3 mesas, suggesting a link between premature chromatin changes and accelerated cell senescence. Canyons mostly form between LADs and are enriched in genes and enhancers. H3K27me3 loss is correlated with up-regulation of key senescence genes, indicating a link between global chromatin changes and local gene expression regulation. Lamin B1 reduction in proliferating cells triggers senescence and formation of mesas and canyons. Our data illustrate profound chromatin reorganization during senescence and suggest that lamin B1 down-regulation in senescence is a key trigger of global and local chromatin changes that impact gene expression, aging, and cancer
