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DBR1 Interactors Identification Analysis in TTDN1 KO background

ABSTRACT: DBR1 interactors were identified from HeLa-S cells (WT or TTDN1 KO).

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hela Cell

SUBMITTER: Kyusik Kim

LAB HEAD: Nima Mosammaparast

PROVIDER: PXD042563 | Pride | 2024-08-09

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	57530_80053.pep.xml	Pepxml
	57531_80056.pep.xml	Pepxml
	57532_80054.pep.xml	Pepxml
	57533_80055.pep.xml	Pepxml
	62695_83590.pep.xml	Pepxml

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1 - 5 of 17

Publications

A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy.

Townley Brittany A BA Buerer Luke L Tsao Ning N Bacolla Albino A Mansoori Fadhel F Rusanov Timur T Clark Nathanial N Goodarzi Negar N Schmidt Nicolas N Srivatsan Sridhar Nonavinkere SN Sun Hua H Sample Reilly A RA Brickner Joshua R JR McDonald Drew D Tsai Miaw-Sheue MS Walter Matthew J MJ Wozniak David F DF Holehouse Alex S AS Pena Vladimir V Tainer John A JA Fairbrother William G WG Mosammaparast Nima N

Molecular cell 20230626 13

The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-bindin ...[more]

PMID: 37369199

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TTDN1 Interactors Identification Analysis

Project description:TTDN1 interactors were identified from HeLa-S cells.

2024-08-10 | PXD042581 | Pride

DBR1 Interactors Identification Mass Spectrometry Analysis

Project description:DBR1 interactors were identified from HeLa-S cells.

2024-08-10 | PXD042580 | Pride

The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands

Project description:CpG-islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 possesses an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. Absence of SAMD1 impairs ES cell differentiation processes, leading to mis-regulation of key biological pathways. Together, our work establishes SAMD1 as a novel chromatin regulator acting at unmethylated CGIs.

2021-05-13 | PXD016781 | Pride

A global regulatory mechanism for activating an exon network required for neurogenesis

Project description:The vertebrate and neural-specific SR-related protein nSR100/SRRM4 regulates an extensive program of alternative splicing with critical roles in nervous system development. However, the mechanism by which nSR100 controls its target exons is poorly understood. We demonstrate that nSR100-dependent neural exons are associated with a unique configuration of intronic cis-elements that promote rapid switch-like regulation during neurogenesis. A key feature of this configuration is the insertion of specialized intronic enhancers between polypyrimidine tracts and acceptor sites that bind nSR100 to potently activate exon inclusion in neural cells, while weakening 3' splice site recognition and contributing to exon skipping in non-neural cells. nSR100 further operates by forming multiple interactions with early spliceosome components bound proximal to 3' splice sites. These multifaceted interactions achieve dominance over neural exon silencing mediated by the splicing regulator PTBP1. The results thus illuminate a widespread mechanism by which a critical neural exon network is activated during neurogenesis. RNA-Seq was used to obtain mRNA profiles of various N2A and 293T cell lines from human and mouse, respectively, to investigate the roles of nSR100, Ptbp1 and U2af65 in alternative splicing regulation. PAR-iCLIP and iCLIP experiments followed by high throughput sequencing were conducted to obtain RNA binding profiles of nSR100, PTBP1 and U2af65.

2014-09-11 | E-GEOD-57278 | biostudies-arrayexpress

Identify the interacting proteins of FBXL4 by AP-MS

Project description:Affinity purification coupled with mass spectrometry (AP-MS) is powerful tools to define the interactome for a specific protein bait. Whereas AP-MS results in the identification of proteins that are in a stable complex.Mass spectrometry was performed to identify the interacting proteins of FBXL4 from FBXL4 -containing protein complexes.

2024-05-12 | PXD040601 | Pride

FOXK2 ChIP-seq

Project description:Chromatin immunoprecipitation of FOXK2 (tagged with Flag and His tags) in U2OS cells detected by SOLiD sequencing. ***Correction March 2014: The sample “FOXK2_Dox_treated” has been renamed, it was originally named “FOXK2_rep2”. A new sample “FOXK2_rep2” has been added, with new files. It has come to our attention that one of the FOXK2 ChIP-seq replicates 'FOXK2_rep2' that we used in our paper recent paper (Ji, Z., Donaldson, I.J., Liu, J., Hayes, A., Zeef, L.A.H. and Sharrocks, A.D. (2012) The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation. Mol. Cell. Biol. 32, 385-398. doi:10.1128/MCB.05504-11) was incorrect. The replicate was actually treated with doxorubicin prior to ChIP-seq analysis resulting in the loss of many FOXK2 binding events.***

2011-01-20 | E-MTAB-565 | biostudies-arrayexpress

Polycomb Cbx orthologs mediate the balance between Hematopoietic Stem Cell self-renewal and differentiation

Project description:By genome-wide ChIP-seq analyses we show that Cbx7 and Cbx8 share ~95% of their targets in bone marrow cells. Cbx7 and Cbx8 have only ~200 targets that are not overlapping between the two proteins. These distinct Cbx7 and Cbx8 targets show reciprocal expression patterns along hematopoietic differentiation. Overexpression of empty vector (negative control), flag-Cbx7 and flag-Cbx8 in 5-FU treated bone marrow cells (progenitor and stem cells), followed by 1 week culture and subsequent ChIP using flag-M2 agarose beads.

2012-12-21 | E-GEOD-36658 | biostudies-arrayexpress

Regulation by the RNA-binding protein Unkempt at its effector interface

Project description:How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of ‘dual-purpose’ peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface.

2024-04-11 | PXD050601 | Pride

53BP1 cooperation with the REV7–shieldin complex underpins DNA structure-specific NHEJ

Project description:53BP1 governs a specialized, context-specific branch of the classical non-homologous end joining DNA double-strand break repair pathway. Mice lacking 53bp1 (also known as Trp53bp1) are immunodeficient owing to a complete loss of immunoglobulin class-switch recombination, and reduced fidelity of long-range V(D)J recombination. The 53BP1-dependent pathway is also responsible for pathological joining events at dysfunctional telomeres, and its unrestricted activity in Brca1-deficient cellular and tumour models causes genomic instability and oncogenesis. Cells that lack core non-homologous end joining proteins are profoundly radiosensitive, unlike 53BP1-deficient cells, which suggests that 53BP1 and its co-factors act on specific DNA substrates. Here we show that 53BP1 cooperates with its downstream effector protein REV7 to promote non-homologous end joining during class-switch recombination, but REV7 is not required for 53BP1-dependent V(D)J recombination. We identify shieldin—a four-subunit putative single-stranded DNA-binding complex comprising REV7, c20orf196 (SHLD1), FAM35A (SHLD2) and FLJ26957 (SHLD3)— as the factor that explains this specificity. Shieldin is essential for REV7-dependent DNA end-protection and non-homologous end joining during class-switch recombination, and supports toxic non-homologous end joining in Brca1-deficient cells, yet is dispensable for REV7-dependent interstrand cross-link repair. The 53BP1 pathway therefore comprises distinct double-strand break repair activities within chromatin and single-stranded DNA compartments, which explains both the immunological differences between 53bp1- and Rev7- deficient mice and the context specificity of the pathway.

2018-07-26 | PXD009650 | Pride

The IRE1 interactome in human LS174T colon epithelial cells

Project description:Inositol-Requiring Enzyme (IRE)1 is an evolutionarily conserved sensor protein of the unfolded protein response (UPR). Vertebrates express two distinct paralogues: IRE1α (gene name ERN1) and IRE1β (gene name ERN2). Both proteins have a similar overall structure, with a sensor domain positioned in the endoplasmic reticulum (ER) lumen, and cytoplasmic kinase and endonuclease domains. For IRE1α, it is well-established that a protein folding chaperone called HSPA5 binds to the ER-luminal domain in conditions when the folding load and capacity are balanced. When unfolded proteins accumulate, HSPA5 is recruited to these unfolded proteins to aid in folding, thereby releasing IRE1α. This initiates a chain reaction of dimerization, trans-autophosphorylation and further oligomerization, resulting in an endonuclease-active IRE1α. Activated IRE1α cleaves an intron from the X-box binding protein 1 mRNA in an unusual cytoplasmic splicing reaction, and the resulting frameshift leads to production of a central UPR transcription factor, XBP1S. In contrast to this, IRE1β is far less extensively characterized. It is expressed solely in mucus-producing cells, more specifically goblet cells. Ectopic expression in other cell types such as Hela cells causes rapid cell death, most likely due to unregulated endonuclease activity. Upon aligning the two IRE1 paralogues, it becomes clear that the luminal domain has the lowest homology between the two paralogues, suggesting differences in how activity of either paralogue is tuned in the ER. In this project, we aimed to characterize and compare the IRE1β and IRE1α interactomes in LS174T cells, a cell line that has retained many goblet cell characteristics, to gain more insights into the regulation and downstream activity of IRE1β in a more relevant cellular background.

2023-11-21 | PXD042756 | Pride

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