Interactome of C-terminally truncated CDK6
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): B Cell, Cell Culture
DISEASE(S): Acute Leukemia
SUBMITTER: 
Thorsten Klampfl
LAB HEAD: Karoline Kollmann
PROVIDER: PXD058474 | Pride | 2024-12-19
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 2303005_KO_629.mzML | Mzml | |||
| 2303005_KO_629.mzid.gz | Mzid | |||
| 2303005_KO_629.raw | Raw | |||
| 2303005_KO_629b.mzML | Mzml | |||
| 2303005_KO_629b.mzid.gz | Mzid |
Items per page: 5 1 - 5 of 54 |
Similar Datasets
Project description:The cell cycle kinase CDK6 interacts with a variety of proteins including cyclins and members of the INK4 and Cip/Kip families. These interactions are thought to involve primarily the N-lobe of the protein. Less is known about the role of the C-lobe for the function of CDK6. In this experiment we assessed the function of the C-lobe in CDK6's interaction with transcriptional complexes. We generated cell lines by retroviral over-expression of BCR-ABL1 in bone marrow cells from CDK6 knock-out mice. We then introduced HA-tagged variants of CDK6 - either wildtype CDK6 (CDK6_WT) or a C-terminally truncated variant of CDK6 lacking the last 32 amino acids of the protein (CDK6_delta-C). ChIP was performed with an antibody against the HA tag. CDK6 KO cell lines were used as controls.
2024-06-30 | E-MTAB-13798 | biostudies-arrayexpress
Project description:Sfl1p and Sfl2p are two homologous heat shock factor-type transcriptional regulators that antagonistically control morphogenesis in Candida albicans, while being required for full pathogenesis and virulence. To understand how Sfl1p and Sfl2p exert their function, we combined genome-wide location and expression analyses to reveal their transcriptional targets in vivo together with the associated changes of the C. albicans transcriptome. We show that Sfl1p and Sfl2p bind to the promoter of at least 113 common targets through divergent binding motifs and modulate directly the expression of key transcriptional regulators of C. albicans morphogenesis and/or virulence. Surprisingly, we found that Sfl2p additionally binds to the promoter of 75 specific targets, including a high proportion of hyphal-specific genes (HSGs; HWP1, HYR1, ECE1, others), revealing a direct link between Sfl2p and hyphal development. Data mining pointed to a regulatory network in which Sfl1p and Sfl2p act as both transcriptional activators and repressors. Sfl1p directly represses the expression of positive regulators of hyphal growth (BRG1, UME6, TEC1, SFL2), while upregulating both yeast form-associated genes (RME1, RHD1,YWP1) and repressors of morphogenesis (SSN6, NRG1). On the other hand, Sfl2p directly upregulates HSGs and activators of hyphal growth (UME6, TEC1), while downregulating yeast form-associated genes and repressors of morphogenesis (NRG1, RFG1, SFL1). Using genetic interaction analyses, we provide further evidences that Sfl1p and Sfl2p antagonistically control C. albicans morphogenesis through direct modulation of the expression of important regulators of hyphal growth. Bioinformatic analyses suggest that binding of Sfl1p and Sfl2p to their targets occurs with the co-binding of Efg1p and/or Ndt80p. Indeed, we show that Sfl1p and Sfl2p targets are bound by Efg1p and that both Sfl1p and Sfl2p associate in vivo with Efg1p. Taken together, our data suggest that Sfl1p and Sfl2p act as central M-bM-^@M-^\switch on/offM-bM-^@M-^] proteins to coordinate the regulation of C. albicans morphogenesis. ChIP was performed in 2 independently grown C. albicans sfl1 or sfl2 homozygous mutant strains expressing (sfl1-CaEXP-SFL1-HA or sfl2-CaEXP-SFL2-HA, respectively) or not (sfl1-CaEXP or sfl2-CaEXP, respectively) SFL1-HA or SFL2-HA (-HA, 3'-triple-HA-tagged alleles of SFL1 or SFL2) under the control of a methionine-repressible promoter (Total samples = 8; 2xCaEXP-SFL1-HA, 2xCaEXP-SFL2-HA, 2xCaEXP control for SFL1-HA ChIP and 2xCaEXP control for SFL2-HA ChIP).
2013-06-15 | E-GEOD-42886 | biostudies-arrayexpress
Project description:The goal of this study was to identify small RNA-ARGONAUTE interactions in Arabidopsis. Co-immunoprecipitation assays followed by high-throughput sequencing were done to identify small RNA associated with HA-AGO2 and HA-AGO7. Experiment Overall Design: Sequencing-by-synthesis technology was used to sequence small RNA from input and co-immunoprecipitation fractions from cell lysates of inflorescence tissue from Arabidopsis plants transformed with HA epitope-tagged AGO2 or AGO7 constructs. Meaningful intepretation requires comparison between the input and co-immunoprecipitation datasets. Experiment Overall Design: Note: Raw data files requested, however, the submitter declined to provide them.
2009-08-30 | E-GEOD-12037 | biostudies-arrayexpress
Project description:C.elegans small RNAs from HA::ALG-1, HA::ALG-2 and HA::RDE-1 IP and rde-1 mutants Small RNAs were cloned from transgenic or mutant C. elegans adults. Sequencing was performed using 454 and Illumina platforms.
2010-04-14 | E-GEOD-20649 | biostudies-arrayexpress
Project description:CarD is an essential mycobacterial protein that we had previously shown to bind the RNA polymerase (RNAP) and affect the transcriptional profile of M. smegmatis and Mycobacterium tuberculosis. For this reason, we suspected that CarD was directly regulating transcriptional complexes but we did not know at what stage of CarD was functioning and at which genes CarD interacted with the RNAP. To determine in which stage of the transcription cycle (initiation, elongation, or termination) CarD acts, we used Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. Specific antibodies targeting core RNAPb, RNAPσ, or a hemagglutinin (HA) epitope fused to CarD (CarD-HA) were used to co-immunoprecipitate associated DNA. CarD-HA was immunoprecipitated from the M. smegmatis Mc2155 ΔcarD attB::tetcarD-HA strain and unfused HA was immunoprecipitated from the Mc2155 attB::pmsg431 strain with monoclonal antibodies specific for HA (Sigma). RNAP β and σ were immunoprecipitated from M. smegmatis ΔcarD attB::tetcarD-HA with monoclonal antibodies specific for these subunits (Neoclone, Madison, WI; 8RB13 for β, 2G10 for σ). Co-precipitated DNA was sequenced using a SOLiD sequencer (Life Technologies), which provided sufficient reads for 100-fold coverage of the genome. The number of sequence reads per base pair was normalized to the total number of reads and expressed as a log2 value. The reads per base pair from the HA-alone sample served as the background and was subtracted from the other datasets. We found that CarD was never present on the genome in the absence of RNAP. However, whereas RNAP core enzyme was found throughout transcribed regions of the genome, CarD was primarily associated with promoter regions and highly correlated with RNAPσ. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. The genome sequences associated with M. smegmatis CarD, RNAPb, and RNAPs were determined by ChIP-seq analysis. Samples were done in duplicate, except for RNAPs. And sequencing was performed using a SOLiD sequencer (Life Technologies).
2013-08-01 | E-GEOD-48164 | biostudies-arrayexpress
Project description:Pre/pro-B-cell lines were generated from bone marrow cells of Cdk6-/- mice by retroviral overexpression of the BCR-ABL (p185) fusion oncogene. These cell lines were transduced with constructs expressing HA-tagged versions of wildtype Cdk6 or of a C-terminally truncated variant of Cdk6 (HA-Cdk6-ΔC). Given the role of CDK6 in transcriptional regulation, we studied the phosphorylation of proteins associated with the chromatin (the phosphochromatome) using phospho-proteomics in cell lines that expressed C-terminally truncated CDK6, wildtype CDK6, or that had a CDK6 knock-out.
2024-12-19 | PXD059037 | Pride
Project description:To find out the binding partners of EhRacJ, crosslinking and coimmunoprecipitation were performed. Then, eluted samples were submitted to Mass Spectrometry and Proteomics Core Facility, Johns Hopkins University School of Medicine and analyzed by mass spctrometry (shotgun proteomics). The coimmunoprecipitation and following analysis were conducted only a single time. You can find data of HA-EhRacJ from "2023_3_13_28_AM_FileSize_1261863517_Byte_F012933.mzid.gz", "2023_3_13_28_AM_FileSize_1261863517_Byte_F012933.mzid_2023_3_13_28_AM_File_Size__1261863517__Byte__F012933.MGF", "JS-E480-CS_230524_NozakiT_MS_DDA_S1_10pct.msf", "JS-E480-CS_230524_NozakiT_MS_DDA_S1_10pct.mzML", and "JS-E480-CS_230524_NozakiT_MS_DDA_S1_10pct.RAW". You can find data of pEhEx-HA (mock) from "2023_6_54_27_PM_FileSize_1168419053_Byte_F012936.mzid.gz", "2023_6_54_27_PM_File Size_1168419053_Byte_F012936.mzid_2023_6_54_27_PM_File_Size__1168419053__Byte__F012936.MGF", "JS-E480-CS_230524_NozakiT_MS_DDA_S4_10pct.msf", "JS-E480-CS_230524_NozakiT_MS_DDA_S4_10pct.mzML", and "JS-E480-CS_230524_NozakiT_MS_DDA_S4_10pct.RAW".
2024-06-20 | PXD051913 | Pride
Project description:We undertook ChIP-Seq of HA-tagged EBNA3A in Lymphoblastoid Cell Lines to understand the effects of this essential viral transcription factor on the cell DNA. We discovered that EBNA3A bound to DNA with BATF, IRF4 and RUNX3, making these Transcription Factors the ones that tether EBNA3A to DNA, allowing it to mediate its downstream effects. ChIP-Seq of 2 biological replicates of HA-tagged EBNA3A were performed. Input was obtained by reverse-crosslinking the cross-linked DNA
2015-01-06 | E-GEOD-59181 | biostudies-arrayexpress
Project description:To find out the binding partners of EhRacM, crosslinking and coimmunoprecipitation were performed. Then, eluted samples were submitted to Mass Spectrometry and Proteomics Core Facility, Johns Hopkins University School of Medicine and analyzed by mass spctrometry (shotgun proteomics). The coimmunoprecipitation and following analysis were conducted three times.You can find the data of HA-EhRacM (1st) from "2022_7_32_54_PM_FileSize_500998639_Byte_F010303.mzid.gz", "2022_7_32_54_PM_FileSize_500998639_Byte_F010303.mzid_2022_7_32_54_PM_File_Size__500998639__Byte__F010303.MGF", "RO-CS-LE_220912_NozakiT_MS_Rac16_WT.mzML", and "RO-CS-LE_220912_NozakiT_MS_Rac16_WT.RAW". You can find the data of pEhExHA (mock) (1st) from "2022_5_02_01_AM_FileSize_662636563_Byte_F010297.mzid.gz", "2022_5_02_01_AM_FileSize_662636563_Byte_F010297.mzid_2022_5_02_01_AM_File_Size__662636563__Byte__F010297.MGF", "RO-CS-LE_220912_NozakiT_MS_pEhExHA.mzML", and "RO-CS-LE_220912_NozakiT_MS_pEhExHA.RAW".You can find the data of HA-EhRacM (2nd) from "2022_7_35_46_AM_FileSize_794949236_Byte_F009769.mzid.gz", "2022_7_35_46_AM_FileSize_794949236_Byte_F009769.mzid_2022_7_35_46_AM_File_Size__794949236__Byte__F009769.MGF", "JS-QE-CS_221108_NozakiT_MS_S1_RA.msf", "JS-QE-CS_221108_NozakiT_MS_S1_RA.RAW", "JS-QE-CS_221108_NozakiT_MS_S1_RA.mzML". You can find the data of pEhExHA (mock) (2nd) from "2022_2_58_28_AM_FileSize_846222756_Byte_F009771.mzid.gz", "2022_2_58_28_AM_FileSize_846222756_Byte_F009771.mzid_2022_2_58_28_AM_File_Size__846222756__Byte__F009771.MGF", "JS-QE-CS_221108_NozakiT_MS_S4_RA.msf", "JS-QE-CS_221108_NozakiT_MS_S4_RA.RAW", and "JS-QE-CS_221108_NozakiT_MS_S4_RA.mzML". You can find the data of HA-EhRacM (3rd) from "2023_12_15_11_AM_FileSize_1380630557_Byte_F012916.mzid.gz", "2023_12_15_11_AM_FileSize_1380630557_Byte_F012916.mzid_2023_12_15_11_AM_File_Size__1380630557__Byte__F012916.MGF", "JS-E480-CS_230518_NozakiT_MS_S1_DDA_10pct.msf", "JS-E480-CS_230518_NozakiT_MS_S1_DDA_10pct.mzML", and "JS-E480-CS_230518_NozakiT_MS_S1_DDA_10pct.RAW". You can find the data of pEhExHA (mock) (3rd) from "2023_6_35_51_PM_FileSize_1732075728_Byte_F012915.mzid.gz", "2023_6_35_51_PM_FileSize_1732075728_Byte_F012915.mzid_2023_6_35_51_PM_File_Size__1732075728__Byte__F012915.MGF", "JS-E480-CS_230518_NozakiT_MS_S4_DDA_10pct.msf", "JS-E480-CS_230518_NozakiT_MS_S4_DDA_10pct.mzML", and "JS-E480-CS_230518_NozakiT_MS_S4_DDA_10pct.RAW".
2024-06-20 | PXD042282 | Pride
Project description:To identify direct transcriptional targets of RFX6, we performed chromatin immunoprecipitation of HA epitope tagged RFX6 followed by massively parallel DNA sequencing (ChIP-seq). Using CRISPR/Cas9 gene editing, the HA epitope was inserted into the 3' end of the RFX6 gene in H9 hESC. Pluripotent cells were then differentiated into PDX1+RFX6+ pancreatic progenitors and endogenous RFX6-HA was immunoprecipitated with an anti-HA antibody. To eliminate background signal caused by non-specific antibody binding, a control experiment using wild-type H9 hESC was performed in parallel.
2020-10-23 | E-MTAB-9335 | biostudies-arrayexpress