4.8 Article

Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

Ensembl 2022

Fiona Cunningham et al.

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

NUCLEIC ACIDS RESEARCH (2022)

Review Oncology

Biological function and molecular mechanism of SRSF3 in cancer and beyond

Jian Xiong et al.

Summary: SRSF3, abnormally expressed in tumors, plays important roles in promoting tumorigenesis and cell proliferation, inhibiting cell senescence and apoptosis, and significantly inhibiting the proliferation and metastasis of tumor cells.

ONCOLOGY LETTERS (2022)

Article Biochemistry & Molecular Biology

Regulated splicing of large exons is linked to phase-separation of vertebrate transcription factors

Toshihiko Kawachi et al.

Summary: A set of nearly 3,000 SRSF3-dependent large constitutive exons (S3-LCEs) have been identified in human and mouse cells, which are enriched for cytidine-rich sequence motifs and regulated by splicing factors hnRNP K and SRSF3. These exons are found in genes for transcription machineries and their mis-splicing can disrupt phase-separated assemblies of transcription factors. Cytidine enrichment in large exons introduces proline/serine codon bias in intrinsically disordered regions and is evolutionarily acquired in vertebrates, suggesting a layered splicing regulation by hnRNP K and SRSF3 for proper phase-separation of transcription factors.

EMBO JOURNAL (2021)

Article Biochemistry & Molecular Biology

UniProt: the universal protein knowledgebase in 2021

Alex Bateman et al.

Summary: The UniProt Knowledgebase aims to provide users with a comprehensive, high-quality set of protein sequences annotated with functional information. Updates over the past two years have increased the number of sequences to approximately 190 million, with new methods to assess proteome completeness and quality. UniProtKB has responded to the COVID-19 pandemic by expertly curating relevant entries and making them rapidly available through a dedicated portal.

NUCLEIC ACIDS RESEARCH (2021)

Article Cell Biology

Generic nature of the condensed states of proteins

Monika Fuxreiter et al.

Summary: Proteins undergoing liquid-liquid phase separation are being discovered more frequently, with the liquid condensed state considered a fundamental state of proteins, playing various biological functions.

NATURE CELL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

Sagie Brodsky et al.

MOLECULAR CELL (2020)

Article Biochemistry & Molecular Biology

Why genes in pieces?'revisited

Ben Smithers et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

David T. Jones et al.

BIOINFORMATICS (2015)

Article Cell Biology

Origin of Spliceosomal Introns and Alternative Splicing

Manuel Irimia et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Review Biology

Origin and evolution of spliceosomal introns

Igor B. Rogozin et al.

BIOLOGY DIRECT (2012)

Article Biochemistry & Molecular Biology

Splicing of internal large exons is defined by novel cis-acting sequence elements

Mohan T. Bolisetty et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemical Research Methods

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

Miklos Csuros et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Review Biochemistry & Molecular Biology

The birth of new exons: Mechanisms and evolutionary consequences

Rotem Sorek

Article Biochemical Research Methods

POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions

Shuichi Hirose et al.

BIOINFORMATICS (2007)

Article Biochemistry & Molecular Biology

Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation

Yoshiaki Minezaki et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Multidisciplinary Sciences

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

Pedro R. Romero et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Multidisciplinary Sciences

Introns and the origin of nucleus-cytosol compartmentalization

W Martin et al.

NATURE (2006)

Article Biochemistry & Molecular Biology

Modules, multidomain proteins and organismic complexity

H Tordai et al.

FEBS JOURNAL (2005)

Article Biochemistry & Molecular Biology

Prediction and functional analysis of native disorder in proteins from the three kingdoms of life

JJ Ward et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Review Biochemistry & Molecular Biology

Intrinsically unstructured proteins evolve by repeat expansion

P Tompa

BIOESSAYS (2003)

Review Multidisciplinary Sciences

The structure of the protein universe and genome evolution

EV Koonin et al.

NATURE (2002)

Review Multidisciplinary Sciences

Initial sequencing and analysis of the human genome

ES Lander et al.

NATURE (2001)

Review Biochemistry & Molecular Biology

The impact of comparative genomics on our understanding of evolution

EV Koonin et al.