The disordered regions of SETD2 govern H3K36me3 deposition by regulating its proteasome-mediated decay

ABSTRACTSETD2 is the sole methyltransferase that tri-methylates histone H3 at lysine 36 in mammals. It has an extended N-terminal region which is absent in its yeast homolog Set2. The function of this poorly characterized region in regulating SETD2 stability has been reported. However, how this region regulates SETD2 half-life and the consequences of the cellular accumulation of SETD2 is unclear. Here we show that the SETD2 N-terminal region contains disordered regions and is targeted for degradation by the proteasome. The marked increase in global H3K36me3 that occurs on the removal of the N-terminal segment results in a non-canonical distribution including reduced enrichment over gene bodies and exons. An increased SETD2 abundance leads to widespread changes in transcription and alternative splicing. Thus, the regulation of SETD2 levels through intrinsically disordered region-facilitated proteolysis is important to maintain the fidelity of transcription and splicing related processes.

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The N-terminal region of Jaw1 has a role to inhibit the formation of organized smooth endoplasmic reticulum as an intrinsically disordered region

Scientific Reports ◽

10.1038/s41598-020-80258-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Takuma Kozono ◽

Hiroyuki Sato ◽

Wataru Okumura ◽

Chifuyu Jogano ◽

Miwa Tamura-Nakano ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Protein Interactions ◽

Smooth Endoplasmic Reticulum ◽

Ectopic Expression ◽

Coiled Coil ◽

Terminal Region ◽

Oligomeric State ◽

Intrinsically Disordered ◽

Coiled Coil Domain ◽

Intrinsically Disordered Region

AbstractJaw1/LRMP is a type II integral membrane protein that is localized at the endoplasmic reticulum (ER) and outer nuclear membrane. We previously reported that a function of Jaw1 is to maintain the nuclear shape as a KASH protein via its carboxyl terminal region, a component of linker of nucleoskeleton and cytoskeleton complex in the oligomeric state. Although the oligomerization of some KASH proteins via the cytosolic regions serves to stabilize protein-protein interactions, the issue of how the oligomerization of Jaw1 is regulated is not completely understood. Therefore, we focused on three distinct regions on the cytosolic face of Jaw1: the N-terminal region, the coiled-coil domain and the stem region, in terms of oligomerization. A co-immunoprecipitation assay showed that its coiled-coil domain is a candidate for the oligomerization site. Furthermore, our data indicated that the N-terminal region prevents the aberrant oligomerization of Jaw1 as an intrinsically disordered region (IDR). Importantly, the ectopic expression of an N-terminal region deleted mutant caused the formation of organized smooth ER (OSER), structures such as nuclear karmellae and whorls, in B16F10 cells. Furthermore, this OSER interfered with the localization of the oligomer and interactors such as the type III inositol 1,4,5-triphosphate receptor (IP3R3) and SUN2. In summary, the N-terminal region of Jaw1 inhibits the formation of OSER as an IDR to maintain the homeostatic localization of interactors on the ER membrane.

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Splice junction centric approach to identify translated noncanonical isoforms in the human proteome

10.1101/372995 ◽

2018 ◽

Author(s):

Edward Lau ◽

Yu Han ◽

Maggie P. Y. Lam

Keyword(s):

Alternative Splicing ◽

Rna Sequencing ◽

Splice Site ◽

Splice Junction ◽

Human Proteome ◽

Protein Isoforms ◽

Sequencing Data ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

AbstractRNA sequencing has led to the discovery of many transcript isoforms created by alternative splicing, but the translational status and functional significance of most alternative splicing events remain unknown. Here we applied a splice junction-centric approach to survey the landscape of protein alternative isoform expression in the human proteome. We focused on alternative splice events where pairs of splice junctions corresponding to included and excluded exons with appreciable read counts are translated together into selective protein sequence databases. Using this approach, we constructed tissue-specific FASTA databases from ENCODE RNA sequencing data, then reanalyzed splice junction peptides in existing mass spectrometry datasets across 10 human tissues (heart, lung, liver, pancreas, ovary, testis, colon, prostate, adrenal gland, and esophagus). Our analysis reidentified 1,108 non-canonical isoforms annotated in SwissProt. We further found 253 novel splice junction peptides in 212 genes that are not documented in the comprehensive Uniprot TrEMBL or Ensembl RefSeq databases. On a proteome scale, non-canonical isoforms differ from canonical sequences preferentially at sequences with heightened protein disorder, suggesting a functional consequence of alternative splicing on the proteome is the regulation of intrinsically disordered regions. We further observed examples where isoform-specific regions intersect with important cardiac protein phosphorylation sites. Our results reveal previously unidentified protein isoforms and may avail efforts to elucidate the functions of splicing events and expand the pool of observable biomarkers in profiling studies.Acronyms and AbbreviationsA3SSalternative 3-prime splice site;A5SSalternative 5-prime splice site;FDRfalse discovery rate;IDRintrinsically disordered regions;MXEmutually exclusive exons;PSIpercent spliced in;PTCpremature termination codon;PTMpost-translational modifications;SEskipped exon;RIretained intron.

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Alternative splicing of intrinsically disordered regions and rewiring of protein interactions

Current Opinion in Structural Biology ◽

10.1016/j.sbi.2013.03.006 ◽

2013 ◽

Vol 23 (3) ◽

pp. 443-450 ◽

Cited By ~ 119

Author(s):

Marija Buljan ◽

Guilhem Chalancon ◽

A Keith Dunker ◽

Alex Bateman ◽

S Balaji ◽

...

Keyword(s):

Alternative Splicing ◽

Protein Interactions ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Disordered Regions

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Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region

Physical Chemistry Chemical Physics ◽

10.1039/c5cp06197k ◽

2016 ◽

Vol 18 (8) ◽

pp. 5839-5849 ◽

Cited By ~ 30

Author(s):

Michelle L. Gill ◽

R. Andrew Byrd ◽

Arthur G. Palmer, III

Keyword(s):

Signaling Pathways ◽

Intrinsically Disordered Proteins ◽

Dna Interaction ◽

Disordered Proteins ◽

Intrinsically Disordered ◽

Intrinsically Disordered Regions ◽

Model Free ◽

Intrinsically Disordered Region ◽

Disordered Regions

Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are known to play important roles in regulatory and signaling pathways.

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Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

10.26434/chemrxiv.9874379 ◽

2019 ◽

Author(s):

Duy Phuoc Tran ◽

Akio Kitao

Keyword(s):

Free Energy ◽

Transcriptional Activation ◽

Binding Free Energy ◽

Energy Structure ◽

Induced Fit ◽

Hydrogen Bond Formation ◽

Conformational Selection ◽

Intrinsically Disordered ◽

Intrinsically Disordered Region ◽

Dissociation Mechanisms

<p>We investigate association and dissociation mechanisms of a typical intrinsically disordered region (IDR), transcriptional activation subdomain of tumor repressor protein p53 (TAD-p53) with murine double-minute clone 2 protein (MDM2). Using the combination of cycles of association and dissociation parallel cascade molecular dynamics, multiple standard MD, and Markov state model, we are successful in obtaining the lowest free energy structure of MDM2/TAD-p53 complex as the structure very close to that in crystal without prior knowledge. This method also reproduces the experimentally measured standard binding free energy, and association and dissociation rate constants solely with the accumulated MD simulation cost of 11.675 μs, in spite of the fact that actual dissociation occurs in the order of a second. Although there exist a few complex intermediates with similar free energies, TAD-p53 first binds MDM2 as the second lowest free energy intermediate dominantly (> 90% in flux), taking a form similar to one of the intermediate structures in its monomeric state. The mechanism of this step has a feature of conformational selection. In the second step, dehydration of the interface, formation of π-π stackings of the side-chains, and main-chain relaxation/hydrogen bond formation to complete α-helix take place, showing features of induced fit. In addition, dehydration (dewetting) is a key process for the final relaxation around the complex interface. These results demonstrate a more fine-grained view of the IDR association/dissociation beyond classical views of protein conformational change upon binding.</p>

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