418 research outputs found
Overexpression and alternative splicing of NF-YA in breast cancer
NF-Y is a CCAAT-binding trimeric transcription factor, whose regulome, interactome and oncogenic potential point to direct involvement in cellular transformation. Yet little is known about the levels of NF-Y subunits in tumors. We focused on breast carcinomas, and analyzed RNA-Seq datasets of TCGA and 54 BRCA cell lines at gene and isoforms level. We partitioned all tumors in the four major subclasses. NF-YA, but not histone-fold subunits NF-YB/NF-YC, is globally overexpressed, correlating with the proliferative Ki67 marker and a common set of 840 genes, with cell-cycle, metabolism GO terms. Their promoters are enriched in NF-Y, GC-rich and E2F sites. Surprisingly, there is an isoform switch, with the "short" isoform -NF-YAs- becoming predominant in tumors. E2F genes are also overexpressed in BRCA, but no switch in isoforms is observed. In Basal-like Claudinlow cell lines and tumors, expression of NF-YAl -long- isoform is high, together with 11 typical EMT markers and low levels of basal Keratins. Analysis of Progression-Free-Intervals indicates that tumors with unbalance of NF-YA isoforms ratios have worst clinical outcomes. The data suggest that NF-YA overexpression increases CCAAT-dependent, pro-growth genes in BRCA. NF-YAs is associated with a proliferative signature, but high levels of NF-YAl signal loss of epithelial features, EMT and acquisition of a more aggressive behavior in a subset of Claudinlow Basal-like tumors
The Switch from NF-YAl to NF-YAs Isoform Impairs Myotubes Formation
NF-YA, the regulatory subunit of the trimeric transcription factor (TF) NF-Y, is regulated by alternative splicing (AS) generating two major isoforms, "long" (NF-YAl) and "short" (NF-YAs). Muscle cells express NF-YAl. We ablated exon 3 in mouse C2C12 cells by a four-guide CRISPR/Cas9n strategy, obtaining clones expressing exclusively NF-YAs (C2-YAl-KO). C2-YAl-KO cells grow normally, but are unable to differentiate. Myogenin and-to a lesser extent, MyoD- levels are substantially lower in C2-YAl-KO, before and after differentiation. Expression of the fusogenic Myomaker and Myomixer genes, crucial for the early phases of the process, is not induced. Myomaker and Myomixer promoters are bound by MyoD and Myogenin, and Myogenin overexpression induces their expression in C2-YAl-KO. NF-Y inactivation reduces MyoD and Myogenin, but not directly: the Myogenin promoter is CCAAT-less, and the canonical CCAAT of the MyoD promoter is not bound by NF-Y in vivo. We propose that NF-YAl, but not NF-YAs, maintains muscle commitment by indirectly regulating Myogenin and MyoD expression in C2C12 cells. These experiments are the first genetic evidence that the two NF-YA isoforms have functionally distinct roles
An acetylation-mono-ubiquitination switch on lysine 120 of H2B.
Post-translational modifications (PTMs) of histones are crucial for transcriptional control, defining positive and negative chromatin territories. A switch of opposing functional significance between acetylation and methylation occurs on many residues. Lysine 120 of H2B is modified by two PTMs: ubiquitination, which is required for further trans-tail H3 methylations and elongation, and acetylation, whose role is less clear. ChIP-Seq with MNase I-treated chromatin indicates that H2BK120ac is present on nucleosomes immediately surrounding the TSS of transcribed or poised units, but not in core promoters. In kinetic ChIP analysis of ER-stress inducible genes, H2BK120ac precedes activation and H2B-ub deposition. Using in vitro acetylation assays, pharmacologic inhibition and RNAi, we established that KAT3 is responsible for H2BK120ac. Interestingly, the global levels of H2B-ub decreased in KAT3-inactivated cells. However, RNF20 recruitment was not impaired by KAT3-inactivation. Our data point at acetylation of Lysine 120 of H2B as an early mark of poised or active state and establish a temporal sequence between acetylation and mono-ubiquitination of this H2B residue
Relativistic effects and two-body currents in using out-of-plane detection
Measurements of the reaction were performed
using an 800-MeV polarized electron beam at the MIT-Bates Linear Accelerator
and with the out-of-plane magnetic spectrometers (OOPS). The
longitudinal-transverse, and , and the
transverse-transverse, , interference responses at a missing momentum
of 210 MeV/c were simultaneously extracted in the dip region at Q=0.15
(GeV/c). On comparison to models of deuteron electrodisintegration, the
data clearly reveal strong effects of relativity and final-state interactions,
and the importance of the two-body meson-exchange currents and isobar
configurations. We demonstrate that these effects can be disentangled and
studied by extracting the interference response functions using the novel
out-of-plane technique.Comment: 4 pages, 4 figures, and submitted to PRL for publicatio
A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors
NF-Y is a trimeric transcription factor (TF), binding the CCAAT box element, for which several results suggest a pioneering role in activation of transcription. In this work, we integrated 380 ENCODE ChIP-Seq experiments for 154 TFs and cofactors with sequence analysis, protein-protein interactions and RNA profiling data, in order to identify genome-wide regulatory modules resulting from the co-association of NF-Y with other TFs. We identified three main degrees of co-association with NF-Y for sequence-specific TFs. In the most relevant one, we found TFs having a significant overlap with NF-Y in their DNA binding loci, some with a precise spacing of binding sites with respect to the CCAAT box, others (FOS, Sp1/2, RFX5, IRF3, PBX3) mostly lacking their canonical binding site and bound to arrays of well spaced CCAAT boxes. As expected, NF-Y binding also correlates with RNA Pol II General TFs and with subunits of complexes involved in the control of H3K4 methylations. Co-association patterns are confirmed by protein-protein interactions, and correspond to specific functional categorizations and expression level changes of target genes following NF-Y inactivation. These data define genome-wide rules for the organization of NF-Y-centered regulatory modules, supporting a model of distinct categorization and synergy with well defined sets of TFs
A Measurement of the Interference Structure Function, R_LT, for the 12C(e,e'p) reaction in the Quasielastic Region
The coincidence cross-section and the interference structure function, R_LT,
were measured for the 12C(e,e'p) 11B reaction at quasielastic kinematics and
central momentum transfer of q=400 MeV/c. The measurement was at an opening
angle of theta_pq=11 degrees, covering a range in missing energy of E_m = 0 to
65 MeV. The R_LT structure function is found to be consistent with zero for E_m
> 50 MeV, confirming an earlier study which indicated that R_L vanishes in this
region. The integrated strengths of the p- and s-shell are compared with a
Distorted Wave Impulse Approximation calculation. The s-shell strength and
shape are compared with a Hartree Fock-Random Phase Approximation calculation.
The DWIA calculation overestimates the cross sections for p- and s-shell proton
knockout as expected, but surprisingly agrees with the extracted R_LT value for
both shells. The HF-RPA calculation describes the data more consistently, which
may be due to the inclusion of 2-body currents in this calculation.Comment: 8 Pages LaTex, 5 postscript figures. Submitted to Phys. Rev.
Dysregulation of NFâY splicing drives metabolic rewiring and aggressiveness in colon cancer
NF-Y is an evolutionarily conserved transcription factor that binds specifically to the CCAAT
elements of eukaryotic genes, most of which frequently deregulated in cancer. NF-YA, the
regulatory subunit of the NF-Y complex, has two isoforms generated by alternative splicing,
NF-YAl and NF-YAs, which differ in the transactivation domain.
Transcriptomic data from The Cancer Genome Atlas (TCGA) database highlighted a
significant increase in the expression of NF-YAs at the expense of NF-YAl in colorectal cancer
(CRC), compared to healthy tissues. Despite this, high NF-YAl levels predict lower patientsâ
survival and distinguish the mesenchymal molecular subtype CMS4, which is characterized by
the worst prognosis.
Through the analysis of 3D cellular models, we demonstrated that altered expression of genes
related to extracellular matrix and epithelial-mesenchymal transition sustains enhanced
migratory and invasive behavior of NF-YAl-transduced cells. Moreover, the integration of
metabolomics, bioenergetics and transcriptional analyses demonstrated a direct role for NFYAl
in metabolic flexibility of cancer cells that adjust their metabolism in response to
environmental changes to potentiate migration. The zebrafish xenograft model confirmed the
metastatic potential triggered by NF-YAl in CRC cells.
Altogether, our data highlight the transcriptional role of NF-YAl in CRC aggressiveness and
suggest splice-switching strategies to hinder NF-YAl-induced metastatic dissemination
LTR12 promoter activation in a broad range of human tumor cells by HDAC inhibition
A considerable proportion of the human genome consists of transposable elements, including the long terminal repeats (LTRs) of endogenous retroviruses. During evolution, such LTRs were occasionally inserted upstream of protein-coding genes, contributing to their regulation. We previously identified the LTR12 from endogenous retrovirus 9 (ERV9) as a regulator of proapoptotic genes such as TP63 or TNFRSF10B. The promoter activity of LTR12 is largely confined to the testes, silenced in testicular carcinoma, but reactivated in testicular cancer cells by broad-range histone deacetylase (HDAC) inhibitors. Here we show that inhibition of HDAC1-3 is sufficient for LTR12 activation. Importantly, HDAC inhibitors induce LTR12 activity not only in testicular cancer cells, but also in cells derived from many additional tumor species. Finally, we characterize the transcription factor NF-Y as a mediator of LTR12 promoter activity and HDAC inhibitor-induced apoptosis, in the context of widespread genomic binding of NF-Y to specific LTR12 sequences. Thus, HDAC inhibitor-driven LTR12 activation represents a generally applicable means to induce proapoptotic genes in human cancer cells
Epigenetic regulation of human SOX3 gene expression during early phases of neural differentiation of NT2/D1 cells
Sox3/SOX3 is one of the earliest neural markers in vertebrates. Together with the Sox1/ SOX1 and Sox2/SOX2 genes it is implicated in the regulation of stem cell identity. In the present study, we performed the first analysis of epigenetic mechanisms (DNA methylation and histone marks) involved in the regulation of the human SOX3 gene expression during RA-induced neural differentiation of NT2/D1 cells. We show that the promoter of the human SOX3 gene is extremely hypomethylated both in undifferentiated NT2/D1 cells and during the early phases of RA-induced neural differentiation. By employing chromatin immunoprecipitation, we analyze several histone modifications across different regions of the SOX3 gene and their dynamics following initiation of differentiation. In the same timeframe we investigate profiles of selected histone marks on the promoters of human SOX1 and SOX2 genes. We demonstrate differences in histone signatures of SOX1, SOX2 and SOX3 genes. Considering the importance of SOXB1 genes in the process of neural differentiation, the present study contributes to a better understanding of epigenetic mechanisms implicated in the regulation of pluripotency maintenance and commitment towards the neural lineage
Precise 3D track reconstruction algorithm for the ICARUS T600 liquid argon time projection chamber detector
Liquid Argon Time Projection Chamber (LAr TPC) detectors offer charged
particle imaging capability with remarkable spatial resolution. Precise event
reconstruction procedures are critical in order to fully exploit the potential
of this technology. In this paper we present a new, general approach of
three-dimensional reconstruction for the LAr TPC with a practical application
to track reconstruction. The efficiency of the method is evaluated on a sample
of simulated tracks. We present also the application of the method to the
analysis of real data tracks collected during the ICARUS T600 detector
operation with the CNGS neutrino beam.Comment: Submitted to Advances in High Energy Physic
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