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cis regulatory element

Jun Xu, Rong-Mei Chen, Shu-Qing Chen, Kai Chen, Lin-Meng Tang, De-Hong Yang, Xu Yang, Yong Zhang, Hong-Sheng Song, Yong-Ping Huang
Identification of stage- and tissue-specific cis-regulatory elements will enable more precise genomic editing. In previous studies of the silkworm Bombyx mori, we identified and characterized several tissue and sex-specific cis-regulatory elements using transgenic technology, including a female- and fat body-specific promoter, vitellogenin; testis-specific promoters, Radial spoke head 1 (BmR1) and beta-tubulin 4 (Bmβ4). Here we reported a cis-regulatory element specific for a somatic and germ cell expressed promoter, nanos (Bmnos)...
December 14, 2018: Insect Science
Puja Agrawal, Katelyn E Heimbruch, Sridhar Rao
Gene expression is regulated by numerous elements including enhancers, insulators, transcription factors, and architectural proteins. Regions of DNA distal to the transcriptional start site, called enhancers, play a central role in the temporal and tissue-specific regulation of gene expression through RNA polymerase II. The identification of enhancers and other cis regulatory elements has largely been possible due to advances in next generation sequencing technologies. Enhancers regulate gene expression through chromatin loops mediated by architectural proteins such as YY1, CTCF, the cohesin complex, and LDB1...
December 13, 2018: Comprehensive Physiology
Helena Jaramillo-Mesa, Megan Gannon, Elijah Holshbach, Jincan Zhang, Robyn Roberts, Matthew Buettner, Aurélie M Rakotondrafara
Several viruses encode an internal ribosome entry site (IRES) at the 5' end of their RNA, which, unlike most cellular mRNAs, initiates translation in the absence of a 5' m7GpppG cap. Here we report a uniquely regulated translation enhancer found in the 739-nt long sequence of Triticum mosaic virus leader sequence that distinguishes the preferred initiation site from a plethora of IRES-encoded AUG triplets. Through deletion mutations of the TriMV 5' untranslated region (UTR), we show that the TriMV 5' UTR encodes a cis-acting picornaviral Y16 -X11 -AUG like-motif (with a 16-nt polypyrimidine CU-tract (Y16 ), at a precise, 11-nt distance (X11 ) from the preferred 13th AUG...
December 12, 2018: Journal of Virology
Margarida T G Rosa, Diego M Almeida, Inês S Pires, Daniel da Rosa Farias, Alice G Martins, Luciano Carlos da Maia, António Costa de Oliveira, Nelson J M Saibo, M Margarida Oliveira, Isabel A Abreu
BACKGROUND: SUMOylation is an essential eukaryotic post-translation modification that, in plants, regulates numerous cellular processes, ranging from seed development to stress response. Using rice as a model crop plant, we searched for potential regulatory points that may influence the activity of the rice SUMOylation machinery genes. RESULTS: We analyzed the presence of putative cis-acting regulatory elements (CREs) within the promoter regions of the rice SUMOylation machinery genes and found CREs related to different cellular processes, including hormone signaling...
December 12, 2018: BMC Plant Biology
Asuka Higo, Tomokazu Kawashima, Michael Borg, Mingmin Zhao, Irene López-Vidriero, Hidetoshi Sakayama, Sean A Montgomery, Hiroyuki Sekimoto, Dieter Hackenberg, Masaki Shimamura, Tomoaki Nishiyama, Keiko Sakakibara, Yuki Tomita, Taisuke Togawa, Kan Kunimoto, Akihisa Osakabe, Yutaka Suzuki, Katsuyuki T Yamato, Kimitsune Ishizaki, Ryuichi Nishihama, Takayuki Kohchi, José M Franco-Zorrilla, David Twell, Frédéric Berger, Takashi Araki
Evolutionary mechanisms underlying innovation of cell types have remained largely unclear. In multicellular eukaryotes, the evolutionary molecular origin of sperm differentiation is unknown in most lineages. Here, we report that in algal ancestors of land plants, changes in the DNA-binding domain of the ancestor of the MYB transcription factor DUO1 enabled the recognition of a new cis-regulatory element. This event led to the differentiation of motile sperm. After neo-functionalization, DUO1 acquired sperm lineage-specific expression in the common ancestor of land plants...
December 11, 2018: Nature Communications
Go Oshima, Elizabeth C Poli, Michael J Bolt, Alexandre Chlenski, Martin Forde, Jessica M S Jutzy, Neha Biyani, Mitchell C Posner, Sean P Pitroda, Ralph R Weichselbaum, Nikolai N Khodarev
Expression of 14q32-encoded miRNA is a favorable prognostic factor in patients with metastatic cancer. In this study, we use genomic inhibition of DNA methylation through disruption of DNA methyltransferases DNMT1 and DNMT3B and pharmacologic inhibition with 5-Aza-2'-deoxycytidine (5-Aza-dC, Decitabine) to demonstrate that DNA methylation predominantly regulates expression of metastasis-suppressive miRNA in the 14q32 cluster. DNA demethylation facilitated CCCTC-binding factor (CTCF) recruitment to the Maternally Expressed Gene 3 differentially methylated region (MEG3-DMR), which acts as a cis-regulatory element for 14q32 miRNA expression...
December 11, 2018: Cancer Research
Sarah N Mapelli, Sara Napoli, Giuseppina Pisignano, Ramon Garcia-Escudero, Giuseppina M Carbone, Carlo V Catapano
Motivation: Long noncoding RNAs (lncRNAs) have gained increasing relevance in epigenetic regulation and nuclear functional organization. High-throughput sequencing approaches have revealed frequent noncoding transcription in promoter-proximal regions. However, a comprehensive catalogue of promoter-associated RNAs (paRNAs) and an analysis of the possible interactions with neighboring genes and genomic regulatory elements are missing. Results: Integrating data from multiple cell types and experimental platforms we identified thousands of paRNAs in the human genome...
December 10, 2018: Bioinformatics
Alexander J Nash, Boris Lenhard
Motivation: Clusters of extremely conserved non-coding elements (CNEs) mark genomic regions devoted to cis-regulation of key developmental genes in Metazoa. We have recently shown that their span coincides with that of topologically associating domains (TADs), making them useful for estimating conserved TAD boundaries in the absence of Hi-C data. The standard approach - detecting CNEs in genome alignments and then establishing the boundaries of their clusters - requires tuning of several parameters and breaks down when comparing closely related genomes...
December 7, 2018: Bioinformatics
Boyuan Sun, Jianbo Tu, Qing Liang, Xinyi Cheng, Xiaolan Fan, Ying Li, Richard W R Wallbank, Mingyao Yang
To investigate whether the members of the mammalian Achaete-Scute Complex homologue (ASH) gene family have evolved functional differences, we used the patterning of bristles as a phenotypic marker. Drosophila uses a single genetic locus - the Achaete-Scute Complex - to demarcate the regions of the body where bristles can form. We found 4-5 Achaete-Scute Complex homologue genes (ASH) in the mammalian genome, which are homologous with scute in Drosophila. Although ASH2 and ASH3 have gained new functions during evolution, the function of ASH4 and its evolutionary changes are still unclear...
December 7, 2018: Gene
Jia-Hsin Huang, Ryan Shun-Yuen Kwan, Zing Tsung-Yeh Tsai, Tzu-Chieh Lin, Huai-Kuang Tsai
Changes in cis -regulatory DNA sequences and transcription factor (TF) repertoires provide major sources of phenotypic diversity that shape the evolution of gene regulation in eukaryotes. The DNA-binding specificities of TFs may be diversified or produce new variants in different eukaryotic species. However, it is currently unclear how various levels of divergence in TF DNA-binding specificities or motifs became introduced into the cis -regulatory DNA regions of the genome over evolutionary time. Here, we first estimated the evolutionary divergence levels of TF binding motifs and quantified their occurrence at DNase I-hypersensitive sites...
2018: Frontiers in Genetics
John T Lovell, Jerry Jenkins, David B Lowry, Sujan Mamidi, Avinash Sreedasyam, Xiaoyu Weng, Kerrie Barry, Jason Bonnette, Brandon Campitelli, Chris Daum, Sean P Gordon, Billie A Gould, Albina Khasanova, Anna Lipzen, Alice MacQueen, Juan Diego Palacio-Mejía, Christopher Plott, Eugene V Shakirov, Shengqiang Shu, Yuko Yoshinaga, Matt Zane, Dave Kudrna, Jason D Talag, Daniel Rokhsar, Jane Grimwood, Jeremy Schmutz, Thomas E Juenger
Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci...
December 6, 2018: Nature Communications
Indu Warrier, Nikhil Ram-Mohan, Zeyu Zhu, Ariana Hazery, Haley Echlin, Jason Rosch, Michelle M Meyer, Tim van Opijnen
Efficient and highly organized regulation of transcription is fundamental to an organism's ability to survive, proliferate, and quickly respond to its environment. Therefore, precise mapping of transcriptional units and understanding their regulation is crucial to determining how pathogenic bacteria cause disease and how they may be inhibited. In this study, we map the transcriptional landscape of the bacterial pathogen Streptococcus pneumoniae TIGR4 by applying a combination of high-throughput RNA-sequencing techniques...
December 5, 2018: PLoS Pathogens
Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M Williams, Tatiana Hochgreb-Hagele, Upeka Senanayake, Vanessa Chong-Morrison, Supat Thongjuea, Emmanouela Repapi, Adam Mead, Tatjana Sauka-Spengler
The neural crest (NC) is a transient embryonic stem cell-like population characterized by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that, during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes...
December 3, 2018: Developmental Cell
Anthony Percival-Smith
Drosophila transcription factor (TF) function is phenotypically nonspecific. Phenotypic nonspecificity is defined as one phenotype being induced or rescued by multiple TFs. To explain this unexpected result, a hypothetical world of limited specificity is explored where all TFs have unique random distributions along the genome due to low information content of DNA sequence recognition and somewhat promiscuous cooperative interactions with other TFs. Transcription is an emergent property of these two conditions...
2018: Genetics Research International
Hanan Polansky, Hava Schwab
CBP and p300 are histone acetyltransferase coactivators that control the transcription of numerous genes in humans, viruses, and other organisms. Although two separate genes encode CBP and p300, they share a 61% sequence identity, and they are often mentioned together as p300/CBP. Zhou et al. showed that under hypoxic conditions, HIF1α and the tumor suppressor p53 compete for binding to the limiting p300/CBP coactivator. Jethanandani & Kramer showed that δEF1 and MYOD genes compete for the limited amount of p300/CBP in the cell...
2018: Cellular & Molecular Biology Letters
Christopher J Ott, Alexander J Federation, Logan S Schwartz, Siddha Kasar, Josephine L Klitgaard, Romina Lenci, Qiyuan Li, Matthew Lawlor, Stacey M Fernandes, Amanda Souza, Donald Polaski, Deepti Gadi, Matthew L Freedman, Jennifer R Brown, James E Bradner
Enhancer profiling is a powerful approach for discovering cis-regulatory elements that define the core transcriptional regulatory circuits of normal and malignant cells. Gene control through enhancer activity is often dominated by a subset of lineage-specific transcription factors. By integrating measures of chromatin accessibility and enrichment for H3K27 acetylation, we have generated regulatory landscapes of chronic lymphocytic leukemia (CLL) samples and representative cell lines. With super enhancer-based modeling of regulatory circuits and assessments of transcription factor dependencies, we discover that the essential super enhancer factor PAX5 dominates CLL regulatory nodes and is essential for CLL cell survival...
November 16, 2018: Cancer Cell
Sarah A McClymont, Paul W Hook, Alexandra I Soto, Xylena Reed, William D Law, Samuel J Kerans, Eric L Waite, Nicole J Briceno, Joey F Thole, Michael G Heckman, Nancy N Diehl, Zbigniew K Wszolek, Cedric D Moore, Heng Zhu, Jennifer A Akiyama, Diane E Dickel, Axel Visel, Len A Pennacchio, Owen A Ross, Michael A Beer, Andrew S McCallion
The progressive loss of midbrain (MB) dopaminergic (DA) neurons defines the motor features of Parkinson disease (PD), and modulation of risk by common variants in PD has been well established through genome-wide association studies (GWASs). We acquired open chromatin signatures of purified embryonic mouse MB DA neurons because we anticipated that a fraction of PD-associated genetic variation might mediate the variants' effects within this neuronal population. Correlation with >2,300 putative enhancers assayed in mice revealed enrichment for MB cis-regulatory elements (CREs), and these data were reinforced by transgenic analyses of six additional sequences in zebrafish and mice...
November 29, 2018: American Journal of Human Genetics
Tsung-Lin Tsai, Chen-Chang Su, Ching-Chi Hsieh, Chao-Nan Lin, Hui-Wen Chang, Chen-Yu Lo, Ching-Houng Lin, Hung-Yi Wu
In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis -acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 alter gene expression. For this aim, we analyzed the variations of the cis -acting elements in the 5' and 3' untranslated regions (UTRs) between the PEDV TW, CV777, and other reference strains. We also determined the previously unidentified transcription regulatory sequence (TRS), a sequence motif required for coronavirus transcription, and found that a nucleotide deletion in the TW strain, in comparison with CV777 strain, immediately downstream of the leader core sequence alters the identity between the leader TRS and the body TRS...
November 29, 2018: Genes
Monika Stachowiak, Izabela Szczerbal, Krzysztof Flisikowski
BACKGROUND: The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic transcript levels and can be used to identify underlying cis-regulatory elements. ASE has not yet been intensively studied in pigs. The aim of this investigation was to analyze the differential allelic expression of four genes, PPARA, PPARG, SREBF1, and PPARGC1A, which are involved in the regulation of fat deposition in porcine subcutaneous and visceral fat and longissimus dorsi muscle...
November 29, 2018: BMC Genetics
Gloria Lozano, Rosario Francisco-Velilla, Encarnacion Martinez-Salas
Beyond the general cap-dependent translation initiation, eukaryotic organisms use alternative mechanisms to initiate protein synthesis. Internal ribosome entry site (IRES) elements are cis -acting RNA regions that promote internal initiation of translation using a cap-independent mechanism. However, their lack of primary sequence and secondary RNA structure conservation, as well as the diversity of host factor requirement to recruit the ribosomal subunits, suggest distinct types of IRES elements. In spite of this heterogeneity, conserved motifs preserve sequences impacting on RNA structure and RNA-protein interactions important for IRES-driven translation...
November 28, 2018: Open Biology
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