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ChIP-seq analysis of HN1L protein in SUM159 triple-negative breast cancer cells

ABSTRACT: Purpose: The goal of this study is to identify the role of HN1L protein as a transcription factor or co-factor in regulating TNBC cells. Methods: Due to the unavailability of a ChIP-grade HN1L antibody, we overexpressed FLAG-tagged HN1L in SUM159 cells and performed ChIP using anti-FLAG antibodies. ChIP DNA was prepared into libraries and sequenced by the Epigenomics Core of Weill Cornell Medical College using SR50 lane. Results: ChIP-Seq analysis began with mapping the sequenced reads to the genome. We utilized the Burrows-Wheeler Aligner (BWA) MEM algorithm to align the sequence reads against the human genome GRCh37/hg19 Assembly. We next used the Hypergoemetric Optimization of Motif Enrichment (HOMER) suite of tools to find and annotate peaks, and identify enriched motifs. HN1L showed 2,249 binding peaks from 10k bp upstream to 5k bp downstream of transcription start site (TSS). Conclusions: among the binding peaks 35 genes overlapped with a previously published BCSC gene signature, 10 genes overlapped with the HN1L knockdown gene signature and 8 genes are well established CSC transcription factors. When applying overlapped genes in the STRING10 pathway analysis database , a protein interaction network centered with STAT3 was obtained. STAT3 and FGFR2 peaks were validated by qPCR. Model-based Analysis of ChIP-Seq (MACS) was then used to confirm the peaks found by Hypergeometric Optimization of Motif EnRichment (HOMER) . Besides the binding peaks found in HOMER, another peak was called by MACS within LEPR , and was also validated by qPCR . These findings indicate that HN1L may act as a transcription factor through binding to enhancer regions of STAT3 and other STAT3 regulators.

ORGANISM(S): Homo sapiens

PROVIDER: GSE105446 | GEO | 2017/12/20

SECONDARY ACCESSION(S): PRJNA415189

REPOSITORIES: GEO

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Project description:The motor neuron (MN)–hexamer complex consisting of LIM homeobox 3, Islet-1, and nuclear LIM interactor is a key determinant of motor neuron specification and differentiation. To gain insights into the transcriptional network in motor neuron development, we performed a genome-wide ChIP-sequencing analysis and found that the MN–hexamer directly regulates a wide array of motor neuron genes by binding to the HxRE (hexamer response element) shared among the target genes. Interestingly, STAT3-binding motif is highly enriched in the MN–hexamer–bound peaks in addition to the HxRE. We also found that a transcriptionally active form of STAT3 is expressed in embryonic motor neurons and that STAT3 associates with the MN–hexamer, enhancing the transcriptional activity of the MN–hexamer in an upstream signal-dependent manner. Correspondingly, STAT3 was needed for motor neuron differentiation in the developing spinal cord. Together, our studies uncover crucial gene regulatory mechanisms that couple MN–hexamer and STAT-activating extracellular signals to promote motor neuron differentiation in vertebrate spinal cord. To explain our experimental scheme briefly, we are interested in finding target sites for the dimer of transcription factors Isl1 and Lhx3. To mimic the biological activity of Isl1/Lhx3 dimer, we made Isl1-Lhx3 fusion and found that Isl1-Lhx3 has a potent biological activity in multiple systems (i.e. generation of ectopic motor neurons). Then we made ES cell line that induces Flag-tagged Isl1-Lhx3 expression upon Dox treatment. These *mouse* ES cells differentiate to motor neurons (iMN-ESCs) when treated with Dox following EB formation. To identify genomic binding sites of Isl1-Lhx3 (Flag-tagged), we performed ChIP with Flag antibody (pull down of Flag-Isl1-Lhx3) in ES cells treated with Dox. ChIP with Flag antibody in ES cells treated with vehicle (no Dox) was done as a negative control in parallel, and sequenced along with +Dox sample. We have done these experiments twice (two sets).

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ChIP-seq analysis of HN1L protein in SUM159 triple-negative breast cancer cells

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