BAMQL: a query language for extracting reads from BAM files

Masella, Andre P.; Lalansingh, Christopher M.; Sivasundaram, Pragash; Fraser, Michael; Bristow, Robert G.; Boutros, Paul C.

doi:10.1186/s12859-016-1162-y

Cited by 20 publications

(14 citation statements)

References 3 publications

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“…The visualization was done using dplyr ( https://CRAN.R-project.org/package=dplyr ) and ggplot2 20 . Sequence read numbers were calculated using Samtools 21 software with sorted bam files.…”

Section: Methodsmentioning

confidence: 99%

Regulation of theACE2locus in human airways cells

Lee

Jung

Hennighausen

2020

Preprint

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SARS-CoV-2 infection of human airway epithelium activates genetic programs that lead to progressive hyperinflammation in COVID-19 patients. Here we report on the transcriptomic response of airway epithelium to interferons and its suppression by the JAK inhibitors Baricitinib and Ruxolitinib. There is a debate on the regulation of the conventional versus the novel intronic promoter inducing the short ACE2 isoform. Through RNA-seq and ChIP-seq analyses for activating chromatin marks and Polymerase II, we define the interferon-activated intronic regulatory region. Our results also support that the conventional ACE2 promoter is controlled by interferon.

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Section: Methodsmentioning

confidence: 99%

Regulation of theACE2locus in human airways cells

Lee

Jung

Hennighausen

2020

Preprint

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“…Reads mapped to the mitochondria during whole-genome alignment were extracted using BAMQL (v1.1) 43 using the command: bamql -I -o out_mito_reads.bam -f input_wgs.bam '(chr(M) & mate_chr(M)) | (chr(Y) & after(59000000) & mate_chr(M))';…”

Section: Methodsmentioning

confidence: 99%

Mitochondrial mutations drive prostate cancer aggression

et al. 2017

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Nuclear mutations are well known to drive tumor incidence, aggression and response to therapy. By contrast, the frequency and roles of mutations in the maternally inherited mitochondrial genome are poorly understood. Here we sequence the mitochondrial genomes of 384 localized prostate cancer patients, and identify a median of one mitochondrial single-nucleotide variant (mtSNV) per patient. Some of these mtSNVs occur in recurrent mutational hotspots and associate with aggressive disease. Younger patients have fewer mtSNVs than those who diagnosed at an older age. We demonstrate strong links between mitochondrial and nuclear mutational profiles, with co-occurrence between specific mutations. For example, certain control region mtSNVs co-occur with gain of the MYC oncogene, and these mutations are jointly associated with patient survival. These data demonstrate frequent mitochondrial mutation in prostate cancer, and suggest interplay between nuclear and mitochondrial mutational profiles in prostate cancer.

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“…Genes were categorized as signi cantly differentially expressed with an adjusted p-value (pAdj) below 0.05 and a fold change > 2 for up-regulated genes and a fold change of < -2 for down-regulated ones. Sequence read numbers were calculated using Samtools 22 software with sorted bam les.…”

Section: Jak Inhibitors Suppress the Ifnb-sensing Enhancers In Theacementioning

confidence: 99%

Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors

Lee¹,

Jung²,

Hennighausen³

2020

Preprint

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SARS-CoV-2 infection of human airway epithelium activates genetic programs that lead to progressive hyperinflammation in COVID-19 patients. Here we report on genetic programs activated by interferons and the suppression by Janus kinase (JAK) inhibitors. The angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2 and deciphering its regulation is paramount for understanding the cell tropism of SARS-CoV-2 infection. We identified candidate regulatory elements in the ACE2 locus in human primary airway cells and lung tissue. Activating histone and promoter marks and Pol II loading characterize the intronic dACE2 and define novel candidate enhancers distal to the genuine ACE2 promoter and within additional introns. dACE2, and to a lesser extent ACE2, RNA levels increased in primary cells treated with interferons and this induction was mitigated by JAK inhibitors that are used therapeutically in COVID-19 patients. Our analyses provide insight into ACE2 regulatory elements and highlight JAK inhibitors as suitable tools to suppress interferon-activated genetic programs in bronchial cells.

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BAMQL: a query language for extracting reads from BAM files

Cited by 20 publications

References 3 publications

Regulation of theACE2locus in human airways cells

Regulation of theACE2locus in human airways cells

Mitochondrial mutations drive prostate cancer aggression

Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors

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