scholarly journals Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

2016 ◽  
Author(s):  
Naoki Osato
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Target Genes ◽  
Functional Enrichment ◽  
Expression Level ◽  
Ctcf Binding ◽  
Cellular Functions ◽  
Median Expression ◽  
Transcriptional Target

AbstractBackgroundTranscriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes.ResultsGene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5 – 60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes.ConclusionsHuman putative transcriptional target genes showed significant functional enrichments. Functional enrichments were related to the cellular functions. The normalized number of functional enrichments of human putative transcriptional target genes changed according to the criteria of enhancer-promoter assignments and correlated with the median expression level of the target genes. These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such as DNA binding proteins and DNA sequences of enhancer-promoter interactions.

DISPOM: A DISCRIMINATIVE DE-NOVO MOTIF DISCOVERY TOOL BASED ON THE JSTACS LIBRARY

2013 ◽  
Vol 11 (01) ◽  
pp. 1340006 ◽  
Author(s):  
JAN GRAU ◽  
JENS KEILWAGEN ◽  
ANDRÉ GOHR ◽  
IVAN A. PAPONOV ◽  
STEFAN POSCH ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Motif Discovery ◽  
Binding Proteins ◽  
Target Genes ◽  
De Novo ◽  
Specific Binding ◽  
Dna Binding Proteins ◽  
De Novo Motif Discovery

DNA-binding proteins are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in target regions of genomic DNA. However, de-novo discovery of these binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not yet been solved satisfactorily. Here, we present a detailed description and analysis of the de-novo motif discovery tool Dispom, which has been developed for finding binding sites of DNA-binding proteins that are differentially abundant in a set of target regions compared to a set of control regions. Two additional features of Dispom are its capability of modeling positional preferences of binding sites and adjusting the length of the motif in the learning process. Dispom yields an increased prediction accuracy compared to existing tools for de-novo motif discovery, suggesting that the combination of searching for differentially abundant motifs, inferring their positional distributions, and adjusting the motif lengths is beneficial for de-novo motif discovery. When applying Dispom to promoters of auxin-responsive genes and those of ABI3 target genes from Arabidopsis thaliana, we identify relevant binding motifs with pronounced positional distributions. These results suggest that learning motifs, their positional distributions, and their lengths by a discriminative learning principle may aid motif discovery from ChIP-chip and gene expression data. We make Dispom freely available as part of Jstacs, an open-source Java library that is tailored to statistical sequence analysis. To facilitate extensions of Dispom, we describe its implementation using Jstacs in this manuscript. In addition, we provide a stand-alone application of Dispom at http://www.jstacs.de/index.php/Dispom for instant use.

scholarly journals A direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila

2019 ◽  
Author(s):  
Christopher M. Uyehara ◽  
Daniel J. McKay
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Dna Binding ◽  
Nuclear Receptor ◽  
Binding Sites ◽  
Target Genes ◽  
Transcriptional Responses ◽  
Developmental Transitions ◽  
The Impact

ABSTRACTThe ecdysone pathway was amongst the first experimental systems employed to study the impact of steroid hormones on the genome. In Drosophila and other insects, ecdysone coordinates developmental transitions, including wholesale transformation of the larva into the adult during metamorphosis. Like other hormones, ecdysone controls gene expression through a nuclear receptor, which functions as a ligand-dependent transcription factor. Although it is clear that ecdysone elicits distinct transcriptional responses within its different target tissues, the role of its receptor, EcR, in regulating target gene expression is incompletely understood. In particular, EcR initiates a cascade of transcription factor expression in response to ecdysone, making it unclear which ecdysone-responsive genes are direct EcR targets. Here, we use the larval-to-prepupal transition of developing wings to examine the role of EcR in gene regulation. Genome-wide DNA binding profiles reveal that EcR exhibits widespread binding across the genome, including at many canonical ecdysone-response genes. However, the majority of its binding sites reside at genes with wing-specific functions. We also find that EcR binding is temporally dynamic, with thousands of binding sites changing over time. RNA-seq reveals that EcR acts as both a temporal gate to block precocious entry to the next developmental stage as well as a temporal trigger to promote the subsequent program. Finally, transgenic reporter analysis indicates that EcR regulates not only temporal changes in target enhancer activity but also spatial patterns. Together, these studies define EcR as a multipurpose, direct regulator of gene expression, greatly expanding its role in coordinating developmental transitions.SIGNIFICANCENuclear receptors (NRs) are sequence-specific DNA binding proteins that act as intracellular receptors for small molecules such as hormones. Prior work has shown that NRs function as ligand-dependent switches that initiate a cascade of gene expression changes. The extent to which NRs function as direct regulators of downstream genes in these hierarchies remains incompletely understood. Here, we study the role of the NR EcR in metamorphosis of the Drosophila wing. We find that EcR directly regulates many genes at the top of the hierarchy as well as at downstream genes. Further, we find that EcR binds distinct sets of target genes at different developmental times. This work helps inform how hormones elicit tissue- and temporal-specific responses in target tissues.

scholarly journals EPEN-41. C11orf95-RELA FUSION REGULATES ABERRANT GENE EXPRESSION THROUGH THE UNIQUE GENOMIC BINDING SITES FOR EPENDYMOMA FORMATION

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii316-iii316
Author(s):  
Tatsuya Ozawa ◽  
Syuzo Kaneko ◽  
Mutsumi Takadera ◽  
Eric Holland ◽  
Ryuji Hamamoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Motif Discovery ◽  
Target Genes ◽  
Cultured Cells ◽  
De Novo ◽  
Binding Motif ◽  
Aberrant Gene Expression ◽  
Aberrant Gene

Abstract A majority of supratentorial ependymoma is associated with recurrent C11orf95-RELA fusion (RELAFUS). The presence of RELA as one component of the RELAFUS leads to the suggestion that NF-kB activity is involved in the ependymoma formation, thus being a viable therapeutic target in these tumors. However, the oncogenic role of another C11orf95 component in the tumorigenesis is not still determined. In this study, to clarify the molecular mechanism underlying tumorigenesis of RELAFUS, we performed RELAFUS-ChIP-Seq analysis in cultured cells expressing the RELAFUS protein. Genomic profiling of RELAFUS binding sites pinpointed the transcriptional target genes directly regulated by RELAFUS. We then identified a unique DNA binding motif of the RELAFUS different from the canonical NF-kB motif in de novo motif discovery analysis. Significant responsiveness of RELAFUS but not RELA to the motif was confirmed in the reporter assay. An N-terminal portion of C11orf95 was sufficient to localize in the nucleus and recognizes the unique motif. Interestingly, the RELAFUS peaks concomitant with the unique motif were identified around the transcription start site in the RELAFUS target genes as previously reported. These observations suggested that C11orf95 might have served as a key determinant for the DNA binding sites of RELAFUS, thereby induced aberrant gene expression necessary for ependymoma formation. Our results will give insights into the development of new ependymoma therapy.

Promotes Gene Expression by Disrupting the DNA Binding of the AML1/ETO and HDAC1 Repressor Complex.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4386-4386
Author(s):  
Shujun Liu ◽  
M. I. Klisovic ◽  
T. Shen ◽  
J. Yu ◽  
G. Dai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Enzymatic Activity ◽  
Gene Transcription ◽  
Binding Sites ◽  
Target Genes ◽  
Histone H3 ◽  
Hdac Activity ◽  
Dna Binding Sites ◽  
Repressor Complex

Abstract In t(8;21) AML, the AML1/ETO fusion protein promotes leukemogenesis by recruiting histone deacetylase (HDAC) and silencing target genes important for hematopoiesis. In addition to its anticonvulsant properties, valproic acid (VPA), an eight-carbon branched-chain fatty acid, has shown a significant antitumor activity mediated, at least in part, by inhibition of the HDAC enzymatic activity. The molecular mechanisms through which VPA inhibits HDACs and restore gene expression in cancer cells remain, however, to be fully elucidated. Herein, we showed that in AML1/ETO-positive cells, VPA modulates HDAC activity by releasing HDAC1 and AML1/ETO from the DNA binding sites at concentrations attainable in pts. Nuclear and whole cells extracts were obtained from AML1/ETO-positive Kasumi-1 cells untreated or treated with VPA (0.3 to 3 mM) for 24 hours and subjected to immunoblotting with AML1, ETO or HDAC1 antibody. Decreased levels of HDAC1 was noticed in the nuclear extract, but not in the unfractionated cell lysates following VPA treatment. These changes correlated with a dose-dependent inhibition of HDAC enzymatic activity and global hyperacetylation of histone H3 and H4. Decrease of HDAC1 and AML1/ETO in the nucleus was likely due to dissociation of the repressor complex proteins from DNA and relocation in the cytoplasm as indicated by a “band-depletion” assay. Untreated or VPA treated Kasumi-1 cells were cross-linked with 1% formaldehyde to stabilize the binding of proteins to their target DNA sequences, and subjected to immublotting with HADC1, AML1 or ETO antibody. While free protein can be resolved on a polyacrylamide gel by immunoblotting, high-molecular weight DNA-protein complexes cannot. Following formaldehyde cross-linking, in untreated cells, the AML1/ETO-HDAC1 complex was stabilized onto the DNA binding sites thereby forming a low-mobility DNA-protein complex which resulted in the absence of the corresponding gel band. In contrast, following VPA treatment, high-intensity AML1/ETO and HDAC1 bands were visualized, suggesting a decrease in DNA binding and an increase in the free-pools of the AML1/ETO and HDAC1 proteins. No changes were observed in HDAC1 and AML1/ETO RNA or protein levels in cells not cross-linked with formaldehyde, thereby excluding upregulation of the corresponding genes following VPA treatment. Similar results were confirmed at the promoter of specific AML1/ETO-target genes (i.e., IL-3). Following VPA exposure, decreased levels of HDAC1 and AML1/ETO, and histone H3 and H4 hyperacetylation were detected on the IL-3 promoter by chromatin immunoprecipitation. The functional relevance of these changes was supported by detection of mRNA expression of IL-3, which was otherwise silenced in untreated cells. Notably, the activity of VPA to HDAC1 and AML1/ETO appeared quite specific, as levels of other factors that initiate histone acetylation and/or gene transcription such as HAT1 and Pol II did not decrease, rather increased on the IL-3 promoter. Further, following VPA exposure, we observed posttranslational changes of specific H3 and H4 lysine residues associated with gene transcription (H3K9 and H4K16 acetylation and H3K4 methylation), partial cell differentiation, cell cycle arrest via upregulation of p21 and caspase-induced apoptosis. Taken together, these data suggest VPA as a promising compound for targeting molecular subgroups of AML, especially those in which leukemogenesis is promoted by aberrant HDAC activity.

scholarly journals Hottip Lncrna Reinforces CTCF Defined Chromatin Boundaries and Drives Wnt Target Gene Expression in AML Leukemogenesis

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 277-277
Author(s):  
Huacheng Luo ◽  
Ganqian Zhu ◽  
Tsz Kan Fung ◽  
Yi Qiu ◽  
Mingjiang Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Triple Helix ◽  
Target Gene ◽  
Target Genes ◽  
Ctcf Binding ◽  
Target Gene Expression ◽  
Rna Immunoprecipitation

We reported recently that HOXA locus associated lncRNA, HOTTIP, is highly expressed in AML patients carrying MLL rearrangement and NPM1c+ mutations. The expression of HOTTIP positively correlates with posterior HOXA gene expression and poor patient survival. We further demonstrated that HOTTIP acts as an epigenetic regulator to define oncogenic HOXA topologically associated domain (TAD) and drive HOXA associated leukemic transcription program. However, it remains unclear whether and how HOTTIP lncRNA is involved in remodeling leukemic genome to facilitate AML leukemogenesis. Here, we showed that HOTTIP regulates a fraction of CTCF binding sites (CBSs) in the AML genome by directly interacting with CTCF and its binding motifs. We carried out CTCF ChIP-seq and HOTTIP ChIRP (chromatin isolation by RNA purification)-seq comparing WT and HOTTIP knockout (KO) MOLM13 cells. KO of HOTTIP in MLL-rearranged MOLM13 AML cells specifically impaired CTCF binding sites that were co-occupied by HOTTIP lncRNA, whereas loss of HOTTIP did not affect global CTCF binding. These target genes include posterior HOXA genes and Wnt target genes such as C-MYC, EVI1, AXIN, and TWIST1. Furthermore, we found that HOTTIP interacts with its putative target sites by formation of DNA: RNA hybridization structure triple helix and R-loop in vivo and in vitro. We then carried out DRIP (DNA-RNA immunoprecipitation)-seq and DRIPc(DNA-RNA immunoprecipitation followed by cDNA conversion)-Seq, which utilize a sequence independent but structure-specific S9.6 antibody for DRIP to capture global R-loops, by comparing WT and HOTTIP KO MOLM13 cells. The obtained DRIP-seq and DRIPc-seq data were then incorporated and integrated with the HOTTIP ChIRP-seq and CTCF ChIP-seq data to explore global collaboration between R-loop and HOTTIP associated CTCF binding sites. We found that HOTTIP interacts with CTCF binding motif that defines the TADs and the promoters of the HOTTIP target genes by formation of R-loop or triple helix structure. Loss of HOTTIP disrupted the R-loop formation at promoters and enhancers of the HOTTIP target genes to inhibit their expression. In MLL-rearranged AML genome, in addition to the HOXA locus, CTCF forms leukemic specific TADs that protect aberrant Wnt target genes. Depletion of HOTTIP lncRNA impaired CTCF defined TADs in the Wnt target gene loci and reduced Wnt target gene expression. In contrast, overexpression of Hottip lncRNA (Hottip-Tg) in the mice bone marrow hematopoietic compartment perturbs hematopoietic stem cell (HSC) self-renewal and differentiation leading to AML like disease by reinforcing CTCF defined TADs, enhancing chromatin accessibility within TADs, and upregulating gene transcription in the Wnt target loci. Finally, when we treated HOTTIP expressed primary patient AML cells carrying MLL-rearrangement and their derived PDX mouse model with a canonical Wnt inhibitor, ICG-001, ICG-001 inhibited AML LSC self-renewal in in vitro by LTC-IC assays and in vivo leukemogenesis in the PDX mouse models with an aberrant HOTTIP lncRNA expression, but not in HOTTIP negative/low non-MLL AML samples. Thus, HOTTIP lncRNA and CTCF cooperate to specifically reinforce CTCF defined WNT target locus TADs and drive Wnt target gene expression in the HOTTIP expressed AML. Disclosures No relevant conflicts of interest to declare.

Identification of NOTCH1-Controlled Transcriptional Programs In Human T-Cell Development

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2495-2495
Author(s):  
Giusy Della Gatta ◽  
Alberto Ambesi Impiombato ◽  
Teresa Palomero ◽  
Valeria Tosello ◽  
Pavel Sumazin ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Dna Binding ◽  
Binding Sites ◽  
Target Genes ◽  
Protein Biosynthesis ◽  
T Cell Development ◽  
Cell Development ◽  
Notch1 Signaling ◽  
Significant Enrichment

Abstract Abstract 2495 T-cell Acute Lymphoblastic Leukemia (T-ALL) is an aggressive malignancy characterized by constitutive activation on the NOTCH signaling pathway. The NOTCH1 oncogene encodes a ligand activated transcriptional activator that regulates gene expression in association with the RBPJK DNA binding protein. NOTCH1 signaling is strictly required for thymocyte development and activating mutations resulting in aberrant NOTCH1 signaling are present in over 60% of T-ALLs. Over the last years gene expression profiling studies have identified NOTCH1 as a critical transcriptional regulator of cell growth and metabolism in T-ALL. However, the specific mechanisms that mediate the differential expression of NOTCH1 target genes in T-cell development and T-ALL remains to be elucidated. Here we used ChIP-seq technology to define the complete repertoire of NOTCH1 targets in T-ALL. Furthermore, we performed an integrative analysis of these results in the context of gene expression signatures induced NOTCH1 signaling in T-ALL and in the context of thymocyte development. NOTCH1 ChIP-seq analysis was performed by SOLiD3 ultra deep sequencing of chromatin immunoprecipitates generated with two different anti-NOTCH1 antibodies in HPB-ALL cells, a NOTCH1-mutated T-ALL leukemic cell line with high levels of NOTCH1 signaling. Analysis of the distribution of NOTCH1 binding sites relative to annotated genes (3,078 genes associated to NOTCH1 peaks; MACS ChIP-seq with P< 1e–9) showed that 58% of high confidence NOTCH1 peaks are intragenic, 28% are located in promoter regions and 14% are intergenic. Moreover, detailed analysis of these results showed that NOTCH1 binding is preferentially located in the proximal promoter of target genes and revealed a highly significant enrichment of NOTCH1 peaks located between −1Kb and +1kb from the transcription start site. Motif analysis of DNA sequences occupied by NOTCH1 revealed a high level of enrichment of “CTCCCA” NOTCH/RBPJK DNA binding sites (P<0.0001). Further characterization of NOTCH1/RBPJK DNA binding sequences showed high enrichment of an “ACTACANN” motif adjacent to canonical NOTCH/RBPJK sites (MDSCAN score=5.43) and a marked overrepresentation of paired NOTCH/RBPJK sites. Functional annotation using Gene Ontology analysis indicated a significant enrichment of NOTCH1 targets corresponding to transcriptional regulation and protein biosynthesis (P <0.001). NOTCH1 ChIPseq target genes were characteristically downregulated in T-ALL cells upon inhibition of NOTCH1 signaling with a gamma secretase inhibitor. Moreover, functional annotation of top NOTCH1 regulated targets confirmed the dominance of genes involved in protein biosynthesis and cellular anabolic processes. Next, we analyzed the differential expression of NOTCH1 ChIP-seq targets in different stages of T-cell development. This analysis revealed five distinct clusters of NOTCH1 target genes, which were associated with distinct functional categories such as metabolism, cell cycle and signal transduction (P <0.00001). These results are consistent with a combinatorial model of gene regulation where different transcription factors coordinately interact with NOTCH1 signaling to define distinct patterns of gene expression during T-cell development. In order to identify transcription factors involved in the differential regulation of NOTCH1 target genes we analyzed the presence of transcription factor motifs paired at specific distances with RBPJK sites. This analysis revealed a highly significant enrichment of STAT3, AP1, NKX2.5 and YY-1 binding motifs (P <0.01) in association with NOTCH/RBPJK binding sites. Overall these results unravel a complex combinatorial program involved in the regulation of NOTCH1 target genes and point to a coordinated role for JAK/STAT, MAPK/AP1 and NOTCH1 signaling in T-cell development and T-ALL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals miRNA Mediated Noise Making of 3′UTR Mutations in Cancer

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 545 ◽  
Author(s):  
Wei Wu ◽  
Lingxiang Wu ◽  
Mengyan Zhu ◽  
Ziyu Wang ◽  
Min Wu ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Target Genes ◽  
Expression Profiles ◽  
Tumor Development ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Messenger Rnas ◽  
Cellular Functions ◽  
Mrna Binding

Somatic mutations in 3′-untranslated regions (3′UTR) do not alter amino acids and are considered to be silent in cancers. We found that such mutations can promote tumor progression by altering microRNA (miRNA) targeting efficiency and consequently affecting miRNA–mRNA interactions. We identified 67,159 somatic mutations located in the 3′UTRs of messenger RNAs (mRNAs) which can alter miRNA–mRNA interactions (functional somatic mutations, funcMutations), and 69.3% of these funcMutations (the degree of energy change > 12 kcal/mol) were identified to significantly promote loss of miRNA-mRNA binding. By integrating mRNA expression profiles of 21 cancer types, we found that the expression of target genes was positively correlated with the loss of absolute affinity level and negatively correlated with the gain of absolute affinity level. Functional enrichment analysis revealed that genes carrying funcMutations were significantly enriched in the MAPK and WNT signaling pathways, and analysis of regulatory modules identified eighteen miRNA modules involved with similar cellular functions. Our findings elucidate a complex relationship between miRNA, mRNA, and mutations, and suggest that 3′UTR mutations may play an important role in tumor development.

scholarly journals Functions of Gtf2i and Gtf2ird1 in the developing brain: transcription, DNA-binding, and long term behavioral consequences

2019 ◽  
Author(s):  
Nathan D. Kopp ◽  
Kayla R. Nygaard ◽  
Katherine B. McCullough ◽  
Susan E. Maloney ◽  
Harrison W. Gabel ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Conditioned Fear ◽  
Developing Brain ◽  
Ctcf Binding ◽  
Microdeletion Syndrome ◽  
Behavioral Phenotypes ◽  
Marble Burying ◽  
And Behavior

AbstractGtf2ird1 and Gtf2i may mediate aspects of the cognitive and behavioral phenotypes of Williams Syndrome (WS) – a microdeletion syndrome encompassing these transcription factors (TFs). Knockout mouse models of each TF show behavioral phenotypes. Here we identify their genomic binding sites in the developing brain, and test for additive effects of their mutation on transcription and behavior. Both TFs target constrained chromatin modifier and synaptic protein genes, including a significant number of ASD genes. They bind promoters, strongly overlap CTCF binding and TAD boundaries, and moderately overlap each other, suggesting epistatic effects. We used single and double mutants to test whether mutating both TFs will modify transcriptional and behavioral phenotypes of single Gtf2ird1 mutants. Despite little difference in DNA-binding and transcriptome-wide expression, Gtf2ird1 mutation caused balance, marble burying, and conditioned fear phenotypes. However, mutating Gtf2i in addition to Gtf2ird1 did not further modify transcriptomic or most behavioral phenotypes, suggesting Gtf2ird1 mutation alone is sufficient.

scholarly journals Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents

2021 ◽  
Author(s):  
Weizheng Liang ◽  
Guipeng Li ◽  
Huanhuan Cui ◽  
Yukai Wang ◽  
Wencheng Wei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Dna Binding ◽  
Target Genes ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Protein Sequence Analysis ◽  
Functional Differences ◽  
Transcriptional Effect

Abstract Background: Differences in gene expression, which arises from divergence in cis-regulatory elements or alterations in transcription factors (TFs) binding specificity, are one of the most important causes of phenotypic diversity during evolution. On one hand, changes in the cis-elements located in the vicinity of target genes affect TF binding and/or local chromatin environment, thereby modulating gene expression in one-to-one manner. On the other hand, alterations in trans-factors influence the expression of their target genes in a more pleiotropic fashion. Although evolution of amino acid sequences is much slower than that of non-coding regulatory elements, particularly for the TF DNA binding domains (DBD)， it is still possible that changes in TF-DBD might have the potential to drive large phenotypic changes if the resulting effects have a net positive effect on the organism’s fitness. If so, species-specific changes in TF-DBD might be positively selected. So far, however, this possibility has been largely unexplored.Results: By protein sequence analysis, we observed high sequence conservation in the DNA binding domain (DBD) of the transcription factor Cdx2 across many vertebrates, whereas three amino acid changes were exclusively found in mouse Cdx2 (mCdx2), suggesting potential positive selection in the mouse lineage. Multi-omics analyses were then carried out to investigate the effects of these changes. Surprisingly, there were no significant functional differences between mCdx2 and its rat homologue (rCdx2), and none of the three amino acid changes had any impact on its function. Finally, we used rat-mouse allodiploid embryonic stem cells (RMES) to study the cis effects of Cdx2-mediated gene regulation between the two rodents. Interestingly, whereas Cdx2 binding is largely divergent between mouse and rat, the transcriptional effect induced by Cdx2 is conserved to a much larger extent.Conclusions: There were no significant functional differences between mCdx2 and its rat homologue (rCdx2), and none of the three amino acid changes had any impact on its function. Moreover, Cdx2 binding is largely divergent between mouse and rat, the transcriptional effect induced by Cdx2 is conserved to a much larger extent.

Sign in / Sign up

Export Citation Format

Share Document