Evolution of cis-Regulatory Sequences in Drosophila

Transcription factors are proteins that directly bind to regulatory sequences of genes to modulate and adjust plants’ responses to different stimuli including biotic and abiotic stresses. Sedentary plant parasitic nematodes, such as beet cyst nematode, Heterodera schachtii, have developed molecular tools to reprogram plant cell metabolism via the sophisticated manipulation of genes expression, to allow root invasion and the induction of a sequence of structural and physiological changes in plant tissues, leading to the formation of permanent feeding sites composed of modified plant cells (commonly called a syncytium). Here, we report on the AtMYB59 gene encoding putative MYB transcription factor that is downregulated in syncytia, as confirmed by RT-PCR and a promoter pMyb59::GUS activity assays. The constitutive overexpression of AtMYB59 led to the reduction in A. thaliana susceptibility, as indicated by decreased numbers of developed females, and to the disturbed development of nematode-induced syncytia. In contrast, mutant lines with a silenced expression of AtMYB59 were more susceptible to this parasite. The involvement of ABA in the modulation of AtMYB59 gene transcription appears feasible by several ABA-responsive cis regulatory elements, which were identified in silico in the gene promoter sequence, and experimental assays showed the induction of AtMYB59 transcription after ABA treatment. Based on these results, we suggest that AtMYB59 plays an important role in the successful parasitism of H. schachtii on A. thaliana roots.

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Molecular Evolution at the decapentaplegic Locus in Drosophila

Genetics ◽

10.1093/genetics/145.2.297 ◽

1997 ◽

Vol 145 (2) ◽

pp. 297-309 ◽

Cited By ~ 3

Author(s):

Stuart J Newfeld ◽

Richard W Padgett ◽

Seth D Findley ◽

Brent G Richter ◽

Michele Sanicola ◽

...

Keyword(s):

Molecular Evolution ◽

Transforming Growth Factor ◽

Transforming Growth Factor Β ◽

Selective Constraint ◽

Amino Acid Sequences ◽

Regulatory Sequences ◽

Protein Coding ◽

Terminal Ligand ◽

Cdna Sequences ◽

Interspecific Comparisons

Using an elaborate set of cis-regulatory sequences, the decapentaplegic (dpp) gene displays a dynamic pattern of gene expression during development. The C-terminal portion of the DPP protein is processed to generate a secreted signaling molecule belonging to the transforming growth factor-β (TGF-β) family. This signal, the DPP ligand, is able to influence the developmental fates of responsive cells in a concentration-dependent fashion. Here we examine the sequence level organization of a significant portion of the dpp locus in Drosophila melanogaster and use interspecific comparisons with D. simulans, D. pseudoobscura and D.virilis to explore the molecular evolution of the gene. Our interspecific analysis identified significant selective constraint on both the nucleotide and amino acid sequences. As expected, interspecific comparison of protein coding sequences shows that the C-terminal ligand region is highly conserved. However, the central portion of the protein is also conserved, while the N-terminal third is quite variable. Comparison of noncoding regions reveals significant stretches of nucleotide identity in the 3′ untranslated portion of exon 3 and in the intron between exons 2 and 3. An examination of cDNA sequences representing five classes of dpp transcripts indicates that these transcripts encode the same polypeptide.

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Characterisation of novel regulatory sequences compatible with modular assembly in the diatom Phaeodactylum tricornutum

Algal Research ◽

10.1016/j.algal.2020.102159 ◽

2021 ◽

Vol 53 ◽

pp. 102159

Author(s):

Matthias Windhagauer ◽

Raffaela M. Abbriano ◽

Justin Ashworth ◽

Lorenzo Barolo ◽

Ana Cristina Jaramillo-Madrid ◽

...

Keyword(s):

Phaeodactylum Tricornutum ◽

Regulatory Sequences ◽

Modular Assembly

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Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model

Scientific Reports ◽

10.1038/s41598-021-86395-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jiayue-Clara Jiang ◽

Joseph A. Rothnagel ◽

Kyle R. Upton

Keyword(s):

Breast Cancer ◽

Transcription Factor ◽

Transcriptional Regulation ◽

Disease Diagnosis ◽

Integrated Analysis ◽

Regulatory Sequences ◽

Cancer Model ◽

Mcf7 Cells ◽

Epithelial Cancers ◽

Breast Cancer Model

AbstractWhile transposons are generally silenced in somatic tissues, many transposons escape epigenetic repression in epithelial cancers, become transcriptionally active and contribute to the regulation of human gene expression. We have developed a bioinformatic pipeline for the integrated analysis of transcription factor binding and transcriptomic data to identify transposon-derived promoters that are activated in specific diseases and developmental states. We applied this pipeline to a breast cancer model, and found that the L1PA2 transposon subfamily contributes abundant regulatory sequences to co-ordinated transcriptional regulation in breast cancer. Transcription factor profiling demonstrates that over 27% of L1PA2 transposons harbour co-localised binding sites of functionally interacting, cancer-associated transcription factors in MCF7 cells, a cell line used to model breast cancer. Transcriptomic analysis reveals that L1PA2 transposons also contribute transcription start sites to up-regulated transcripts in MCF7 cells, including some transcripts with established oncogenic properties. In addition, we verified the utility of our pipeline on other transposon subfamilies, as well as on leukemia and lung carcinoma cell lines. We demonstrate that the normally quiescent regulatory activities of transposons can be activated and alter the cancer transcriptome. In particular, the L1PA2 subfamily contributes abundant regulatory sequences, and likely plays a global role in modulating breast cancer transcriptional regulation. Understanding the regulatory impact of L1PA2 on breast cancer genomes provides additional insights into cancer genome regulation, and may provide novel biomarkers for disease diagnosis, prognosis and therapy.

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Role of Transposable Elements in Gene Regulation in the Human Genome

Life ◽

10.3390/life11020118 ◽

2021 ◽

Vol 11 (2) ◽

pp. 118

Author(s):

Arsala Ali ◽

Kyudong Han ◽

Ping Liang

Keyword(s):

Gene Regulation ◽

Transposable Elements ◽

Regulatory Sequences ◽

Rna Sequences ◽

Expression Of Genes ◽

Wide Range ◽

Lineage Specificity ◽

Regulatory Rnas ◽

Potential Factors ◽

Interspersed Repeats

Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.

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