Topic
Integrator complex
About: Integrator complex is a research topic. Over the lifetime, 104 publications have been published within this topic receiving 72884 citations.
Papers published on a yearly basis
Papers
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Abstract: In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
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75,888 citations
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Availability: http://samtools.sourceforge.net
Contact: [email protected]
60,749 citations
TL;DR: It is suggested that CBP/p300 serves as an integrator of multiple signal transduction pathways within the nucleus, in addition to distinct coactivators for function of nuclear receptors, CREB, and AP-1.
2,258 citations
TL;DR: An RNA polymerase II complex that contains at least 12 novel subunits, termed the Integrator, in addition to core RNAPII subunits is described, which shows that Integrator is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing.
540 citations
TL;DR: These studies provide the first direct experimental evidence that CPSF-73 is the pre-mRNA 3′-end-processing endonuclease.
Abstract: The crystal structure of CPSF-73, part of a complex involved in mRNA cleavage and polyadenylation is solved. CPSF-73 was purified and shown to endonucleolytically cleave mRNA, in a reaction mediated by two zinc ligands. Most eukaryotic messenger RNA precursors (pre-mRNAs) undergo extensive maturational processing, including cleavage and polyadenylation at the 3′-end1,2,3,4,5,6,7,8. Despite the characterization of many proteins that are required for the cleavage reaction, the identity of the endonuclease is not known4,9,10. Recent analyses indicated that the 73-kDa subunit of cleavage and polyadenylation specificity factor (CPSF-73) might be the endonuclease for this and related reactions10,11,12,13,14,15, although no direct data confirmed this. Here we report the crystal structures of human CPSF-73 at 2.1 A resolution, complexed with zinc ions and a sulphate that might mimic the phosphate group of the substrate, and the related yeast protein CPSF-100 (Ydh1) at 2.5 A resolution. Both CPSF-73 and CPSF-100 contain two domains, a metallo-β-lactamase domain and a novel β-CASP (named for metallo-β-lactamase, CPSF, Artemis, Snm1, Pso2) domain12. The active site of CPSF-73, with two zinc ions, is located at the interface of the two domains. Purified recombinant CPSF-73 possesses RNA endonuclease activity, and mutations that disrupt zinc binding in the active site abolish this activity. Our studies provide the first direct experimental evidence that CPSF-73 is the pre-mRNA 3′-end-processing endonuclease.
479 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2021 | 15 |
| 2020 | 13 |
| 2019 | 13 |
| 2018 | 6 |
| 2017 | 8 |
| 2016 | 2 |