CGAT: computational genomics analysis toolkit

Sims, David; Ilott, Nicholas E.; Sansom, Stephen N.; Sudbery, Ian; Johnson, Jethro; Fawcett, Katherine A.; Berlanga‐Taylor, Antonio J.; Sebastian, Luna-Valero,; Ponting, Chris P.; Heger, Andreas

doi:10.1093/bioinformatics/btt756

Cited by 77 publications

(66 citation statements)

References 13 publications

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“…The CGAT tool kit (version 0.2.5) 40 was used to generate the metagene profiles for the 3′-poly(A) reads and ChIP-seq data. For 3′-poly(A) reads from U1 AMO RNA-seq data, downloaded nongenomic 3′-poly(A) sites from gene body regions (except last exon) in four different human tissues 12 were pooled into 3′-poly(A) sites defined as internal/gene body tissue poly(A)s. To draw a metagene profile of 3′-poly(A) reads from U1 AMO RNA-seq on the internal/gene body tissue poly(A) site, genes were required to have at least one PCPA site by PCPA calculation and one tissue poly(A) site, total 1,166 genes with 2,114 unique poly(A) sites.…”

Section: Methodsmentioning

confidence: 99%

U1 snRNP telescripting regulates a size–function-stratified human genome

Venters

et al. 2017

Nat Struct Mol Biol

104

139

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U1 snRNP (U1) functions in splicing introns and telescripting, which suppresses premature cleavage and polyadenylation (PCPA). Using U1 inhibition in human cells, we show that U1 telescripting is selectively required for sustaining long-distance transcription elongation in introns of large genes (median 39 kb). Evidence of widespread PCPA in the same locations in normal tissues reveals that large genes incur natural transcription attrition. Underscoring the importance of U1 telescripting as a gene-size-based mRNA-regulation mechanism, small genes were not sensitive to PCPA, and the spliced-mRNA productivity of ~1,000 small genes (median 6.8 kb) increased upon U1 inhibition. Notably, these small, upregulated genes were enriched in functions related to acute stimuli and cell-survival response, whereas genes subject to PCPA were enriched in cell-cycle progression and developmental functions. This gene size–function polarization increased in metazoan evolution by enormous intron expansion. We propose that telescripting adds an overarching layer of regulation to size–function-stratified genomes, leveraged by selective intron expansion to rapidly shift gene expression priorities.

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Section: Methodsmentioning

confidence: 99%

U1 snRNP telescripting regulates a size–function-stratified human genome

Venters

et al. 2017

Nat Struct Mol Biol

104

139

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“…3B; Sims et al 2014). As described in full in the Supplemental Methods, per-gene local FDRs (Efron 2005) were estimated using FPKM values quantitated on gene models and on a matched null set of gene models shifted into selected intergenic space.…”

Section: Rna-seq and Local Fdr Analysis Of Gene Expression In Thymic mentioning

confidence: 99%

Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

et al. 2014

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Promiscuous gene expression (PGE) by thymic epithelial cells (TEC) is essential for generating a diverse T cell antigen receptor repertoire tolerant to self-antigens, and thus for avoiding autoimmunity. Nevertheless, the extent and nature of this unusual expression program within TEC populations and single cells are unknown. Using deep transcriptome sequencing of carefully identified mouse TEC subpopulations, we discovered a program of PGE that is common between medullary (m) and cortical TEC, further elaborated in mTEC, and completed in mature mTEC expressing the autoimmune regulator gene (Aire). TEC populations are capable of expressing up to 19,293 protein-coding genes, the highest number of genes known to be expressed in any cell type. Remarkably, in mouse mTEC, Aire expression alone positively regulates 3980 tissue-restricted genes. Notably, the tissue specificities of these genes include known targets of autoimmunity in human AIRE deficiency. Led by the observation that genes induced by Aire expression are generally characterized by a repressive chromatin state in somatic tissues, we found these genes to be strongly associated with H3K27me3 marks in mTEC. Our findings are consistent with AIRE targeting and inducing the promiscuous expression of genes previously epigenetically silenced by Polycomb group proteins. Comparison of the transcriptomes of 174 single mTEC indicates that genes induced by Aire expression are transcribed stochastically at low cell frequency. Furthermore, when present, Aire expression-dependent transcript levels were 16-fold higher, on average, in individual TEC than in the mTEC population.

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“…For unambiguous counting of mapped reads with exon/intron resolution rather than transcript/gene levels, a single transcript was selected per gene using CGAT scripts (version 0.3.2) (Sims, Ilott et al, 2014) with the following parameters: gtf2gtf --method=filter --filter-method=representative-transcript. In these parameters, the "representative transcript" that shared the most exons with the other transcripts in the same gene was used.…”

Section: Bioinformatics Analyses Of Rna-seq Datamentioning

confidence: 99%

LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

Ninomiya

Adachi

Natsume

et al. 2019

Preprint

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A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane‐less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate‐specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII‐Comprehensive identification of RNA‐binding proteins by mass spectrometry (ChIRP‐MS) analysis identified multiple splicing factors in nSBs, including serine and arginine‐rich pre‐mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly de‐phosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re‐phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII‐dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.

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CGAT: computational genomics analysis toolkit

Cited by 77 publications

References 13 publications

U1 snRNP telescripting regulates a size–function-stratified human genome

U1 snRNP telescripting regulates a size–function-stratified human genome

Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation

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