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Transcriptome-wide survey of Runx1-interacting RNAs by RNA immunoprecipitation sequencing

ABSTRACT: Transcriptome-wide survey of Runx1-interacting RNAs by RNA immunoprecipitation sequencing

PROVIDER: PRJNA589846 | ENA |

REPOSITORIES: ENA

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Transcriptome-wide survey of Runx1-interacting RNAs by RNA immunoprecipitation sequencing

Project description:Runt-related transcription factor 1 (RUNX1) plays critical roles in hematopoiesis including myeloid development. Runx1 binds Runt consensus motifs at promoters and regulatory elements of its target genes. Interestingly, several Runx1-binding RNA aptamers have been successfully developed. Additionally, mounting evidences suggest that transcription factors are capable of binding to RNAs. In this study, we performed a transcriptome-wide screen for Runx1-interacting RNAs in living cells using fRIP-Seq. Anti-Runx1 antibody was used to capture Runx1 in the monocytic cell line THP-1. RNAs co-immunoprecipitated with Runx1 were sequenced by paired-end massively parallel sequencing and analyzed by HOMER peak calling and annotation algorithms. By doing so, we identified a repertoire of RNAs interacting with Runx1. We further investigate functional role of these interactions in Runx1-mediated transcription regulation.

2021-10-27 | GSE140459 | GEO

iCLIP analysis of EZH2-interacting RNAs

Project description:RNAs directly interacting with EZH2 were isolated from human colorectal HCT116 cells using an in vivo crosslinking and immunoprecipitation strategy (iCLIP, König J et al, Nat Struct Mol Biol 2010) coupled to an ultrasequencing approach.

2012-04-23 | GSE36070 | GEO

iCLIP analysis of EZH2-interacting RNAs

2012-04-23 | E-GEOD-36070 | biostudies-arrayexpress

Identification of small RNAs interacting with LARP7

Project description:Identification of small RNAs interacting with LARP7

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lncRNA TINCR antisense pulldown of interacting RNAs

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HuD interacting circular RNAs in the mouse striatum

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HDAC3 preferentially binds to RUNX1 in t(8;21) AML cells and collaborates with RUNX1 to repress AML1-ETO-mediated transcriptional activation

Project description:Human histone deacetylase 3 (HDAC3) plays an important role in gene transcription in diseased human cells, such as leukemia. The t(8;21) chromosomal translocation is one of the most commonly observed genetic abnormalities associated with acute myeloid leukemia. This translocation generates the AML1-ETO fusion protein between the wild-type RUNX1 transcription factor and wild-type ETO transcriptional corepressor. To better understand the role of HDAC3 in t(8;21) leukemogenesis, the human HDAC3-containing complexes were isolated from stably-transfected HeLa cells by using anti-FLAG immunoprecipitation. The resulting complexes were resolved in SDS-PAGE. The components of the complexes were identified using LC-MS/MS. We report here that the human RUNX1 transcription is a component of the HDAC3 complexes. We demonstrate that HDAC3 and RUNX1 collaboratively repress AML1-ETO-mediated transcription. These results reveal new insight into how AML1-ETO, RUNX1, and HDAC3 crosstalk to deregulate gene transcription in t(8;21) leukemia cells.

2020-02-17 | PXD017230 | Pride

RNAseq of DRBD7-TAP interacting RNAs in Trypanosoma brucei

Project description:RNAseq of DRBD7-TAP interacting RNAs in Trypanosoma brucei

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RUNX1 is a key target gene in t(4;11) leukemias and contributes to gene activation by interacting with the AF4-MLL complex

Project description:The Mixed Lineage Leukemia 1 protein (MLL1) is an important epigenetic regulator required for the maintenance of gene activation during development. MLL1 chromosome translocations produce novel fusion proteins that cause aggressive leukemias in humans. Individual MLL1 fusion proteins have distinct leukemic phenotypes even when expressed in the same cell type, but how this distinction is delineated on a molecular level is poorly understood. Here we highlight a unique molecular mechanism whereby MLL-AF4 specifically activates the RUNX1 gene and the RUNX1 protein interacts with the product of the reciprocal AF4-MLL translocation. These results support a mechanism of leukemic growth whereby two oncogenic fusion proteins cooperate by activating a target gene and then interacting directly with its downstream product ChIP-seq using RUNX1 antibody in SEM cells

2013-01-31 | E-GEOD-42075 | biostudies-arrayexpress

Identification of CEBPA and RUNX1 interactors in 3q-rearranged AML

Project description:Chromatin immunoprecipitation with specific isolation of chromatin associated proteins (ChIP-SICAP) was used to identify chromatin-bound interactors of CEBPA and RUNX1 in the 3q-rearranged human myeloid leukemia cell line MUTZ-3.

2021-04-29 | PXD020045 | Pride

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