Illuminating the dark side of the human transcriptome with TAMA Iso-Seq analysis

Ri, Kuo; Cheng, Yuanyuan; Smith, Jacqueline; Archibald, Alan; Burt, David W.

doi:10.1101/780015

Cited by 15 publications

(21 citation statements)

References 36 publications

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“…All Iso-Seq data was first processed using software IsoSeq v3.1 to obtain full-length non-concatemer reads with at least 3 full sequencing passes, which were then mapped to the sheep reference genome GCA_002742125.1 using GMAP version 2018-05-30. TAMA Collapse from the TAMA tool kit 83 was used to generate unique gene and transcript models, which were further merged with RNAseq-based annotation data using TAMA Merge to incorporate any transcript models that were identified by RNAseq but not Iso-Seq. Functional annotation of transcripts was carried out using Trinotate (v3.1.1).…”

Section: Discussionmentioning

confidence: 99%

Circadian clock mechanism driving mammalian photoperiodism

et al. 2020

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The annual photoperiod cycle provides the critical environmental cue synchronizing rhythms of life in seasonal habitats. In 1936, Bünning proposed a circadian-based coincidence timer for photoperiodic synchronization in plants. Formal studies support the universality of this socalled coincidence timer, but we lack understanding of the mechanisms involved. Here we show in mammals that long photoperiods induce the circadian transcription factor BMAL2, in the pars tuberalis of the pituitary, and triggers summer biology through the eyes absent/ thyrotrophin (EYA3/TSH) pathway. Conversely, long-duration melatonin signals on short photoperiods induce circadian repressors including DEC1, suppressing BMAL2 and the EYA3/ TSH pathway, triggering winter biology. These actions are associated with progressive genome-wide changes in chromatin state, elaborating the effect of the circadian coincidence timer. Hence, circadian clock-pituitary epigenetic pathway interactions form the basis of the mammalian coincidence timer mechanism. Our results constitute a blueprint for circadianbased seasonal timekeeping in vertebrates.

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Section: Discussionmentioning

confidence: 99%

Circadian clock mechanism driving mammalian photoperiodism

et al. 2020

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“…RNA-seq reads were stringently mapped using HISAT2 (v.2.0.0) 79 . Transcriptomic data were processed using TAMA 80 . All transcriptomic, homology-based and ab initio evidence were integrated into a consensus gene annotation using EVidenceModeller (v.1.1.1) 81 .…”

Section: Gene Annotationmentioning

confidence: 99%

Six reference-quality genomes reveal evolution of bat adaptations

Jebb

Huang

Pippel

et al. 2020

Nature

274

357

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Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols 1 to generate, to our knowledge, the first reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our 'Tool to infer Orthologs from Genome Alignments' (TOGA) software with de novo and homology gene predictions as well as short-and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identified a basal origin for bats within Scrotifera. Our genome-wide screens revealed positive selection on hearing-related genes in the ancestral branch of bats, which is indicative of laryngeal echolocation being an ancestral trait in this clade. We found selection and loss of immunity-related genes (including pro-inflammatory NF-κB regulators) and expansions of anti-viral APOBEC3 genes, which highlights molecular mechanisms that may contribute to the exceptional immunity of bats. Genomic integrations of diverse viruses provide a genomic record of historical tolerance to viral infection in bats. Finally, we found and experimentally validated bat-specific variation in microRNAs, which may regulate bat-specific gene-expression programs. Our reference-quality bat genomes provide the resources required to uncover and validate the genomic basis of adaptations of bats, and stimulate new avenues of research that are directly relevant to human health and disease 1. With more than 1,400 species identified to date 2 , bats (Chiroptera) account for about 20% of all extant mammal species. Bats are found around the world and successfully occupy diverse ecological niches 1. Their global success is attributed to an extraordinary suite of adaptations 1 including powered flight, laryngeal echolocation, vocal learning, exceptional longevity and a unique immune system that probably enables bats to better tolerate viruses that are lethal to other mammals (such as severe acute respiratory syndrome-related coronavirus, Middle East respiratory syndrome-related coronavirus and Ebola virus) 3. Bats therefore represent important model systems for the study of

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“…Transcripts were assembled with settings -f 0.05 as the threshold for isoforms expression and the gtf-files were merged with stringtie --merge. Assembled transcripts were processed with TAMA tools [47] for ORF detection and BLAST parsing to identify coding regions. We used curated proteins from Uniprot_Swissprot together with proteins from the latest ENSEMBL dog annotation (v100) and selected the longest blast hit from the top 5 hits with an E-value below 10^-10 as the id of the protein.…”

Section: Gene Annotationmentioning

confidence: 99%

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Wang

Wallerman

Arendt

et al. 2020

Preprint

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AbstractHere we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.

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Illuminating the dark side of the human transcriptome with TAMA Iso-Seq analysis

Cited by 15 publications

References 36 publications

Circadian clock mechanism driving mammalian photoperiodism

Circadian clock mechanism driving mammalian photoperiodism

Six reference-quality genomes reveal evolution of bat adaptations

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

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