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https://www.readbyqxmd.com/read/28523015/transcription-factors-in-fungi-tfome-dynamics-three-major-families-and-dual-specificity-tfs
#1
Ekaterina Shelest
Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28522193/ph-triggered-re-assembly-of-nanosphere-to-nanofiber-the-role-of-peptide-conformational-change-for-enhanced-cancer-therapy
#2
Peiqing Liang, Junjiong Zheng, Shulin Dai, Jiayu Wang, Zhaoqing Zhang, Ting Kang, Changyun Quan
pH-triggered conformational change and subsequent re-assembly of nanostructures provide a new strategy in nanomedicine for controlled drug release and enhanced therapy. Here, we reported the development of a novel pH-responsive nano-assembly as a drug carrier from peptide amphiphile (PA) consisting of mimicking peptide and stearic acid moieties. The mimicking peptide is a basic 17-amino acid peptide derived from antennapedia homeodomain, and undergoes a conformational transition of the secondary structure from β-sheet at pH7...
May 15, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28515447/dlx3-interacts-with-gcm1-and-inhibits-its-transactivation-stimulating-activity-in-a-homeodomain-dependent-manner-in-human-trophoblast-derived-cells
#3
Sha Li, Mark S Roberson
The placental transcription factors Distal-less 3 (DLX3) and Glial cell missing-1 (GCM1) have been shown to coordinate the specific regulation of PGF in human trophoblast cell lines. While both factors independently have a positive effect on PGF gene expression, when combined, DLX3 acts as an antagonist to GCM. Despite this understanding, potential mechanisms accounting for this regulatory interaction remain unexplored. We identify physical and functional interactions between specific domains of DLX3 and GCM1 in human trophoblast-derived cells by performing immunoprecipitation and mammalian one hybrid assays...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514754/a-hydrophobic-residue-in-the-tale-homeodomain-of-pbx1-promotes-epithelial-to-mesenchymal-transition-of-gastric-carcinoma
#4
Changyu He, Zhenqiang Wang, Li Zhang, Liyun Yang, Jianfang Li, Xuehua Chen, Jun Zhang, Qing Chang, Yingyan Yu, Bingya Liu, Zhenggang Zhu
Pre-B-cell leukemia homeobox 1 (PBX1) was originally identified as a proto-oncogene in human leukemia. Although this protein has been shown to contribute to cellular development and tumorigenesis, the role of PBX1 in gastric carcinoma (GC) remains unclear. In this study, we observed increased expression of PBX1 in GC tissues compared with adjacent normal tissues. This increase in PBX1 expression levels negatively correlated with HOXB9 mRNA expression and was also associated with malignancy and metastasis. PBX1 promoted proliferation and metastasis of GC cells both in vitro and in vivo...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28507987/pitx2-in-embryonic-and-adult-myogenesis
#5
REVIEW
Francisco Hernandez-Torres, Lara Rodríguez-Outeiriño, Diego Franco, Amelia E Aranega
Skeletal muscle is a heterogeneous tissue that represents between 30 and 38% of the human body mass and has important functions in the organism, such as maintaining posture, locomotor impulse, or pulmonary ventilation. The genesis of skeletal muscle during embryonic development is a process controlled by an elaborate regulatory network combining the interplay of extrinsic and intrinsic regulatory mechanisms that transform myogenic precursor cells into functional muscle fibers through a finely tuned differentiation program...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28500265/acyl-coa-binding-protein-acbp1-modulates-sterol-synthesis-during-embryogenesis
#6
Shiu-Cheung Lung, Pan Liao, Edward Chee-Tak Yeung, An-Shan Hsiao, Yan Xue, Mee-Len Chye
Fatty acids (FAs) and sterols are primary metabolites that exert interrelated functions as structural and signaling lipids. Despite their common syntheses from acetyl-CoA, homeostatic crosstalk remains enigmatic. Six Arabidopsis acyl-CoA-binding proteins (ACBPs) are involved in FA metabolism. ACBP1 interacts with PHOSPHOLIPASE Dα1 and regulates phospholipid composition. Herein, its specific role in negative modulation of sterol synthesis during embryogenesis is reported. ACBP1, likely in a liganded state, interacts with STEROL C4-METHYL OXIDASE1-1 (SMO1-1), a rate-limiting enzyme in the sterol pathway...
May 12, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28493870/functional-male-accessory-glands-and-fertility-in-drosophila-require-novel-ecdysone-receptor
#7
Vandana Sharma, Anuj K Pandey, Ajay Kumar, Snigdha Misra, Himanshu P K Gupta, Snigdha Gupta, Anshuman Singh, Norene A Buehner, Kristipati Ravi Ram
In many insects, the accessory gland, a secretory tissue of the male reproductive system, is essential for male fertility. Male accessory gland is the major source of proteinaceous secretions, collectively called as seminal proteins (or accessory gland proteins), which upon transfer, manipulate the physiology and behavior of mated females. Insect hormones such as ecdysteroids and juvenoids play a key role in accessory gland development and protein synthesis but little is known about underlying molecular players and their mechanism of action...
May 11, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28487409/rice-homeodomain-protein-wox11-recruits-a-histone-acetyltransferase-complex-to-establish-programs-of-cell-proliferation-of-crown-root-meristem
#8
Shaoli Zhou, Wei Jiang, Fei Long, Saifeng Cheng, Wenjing Yang, Yu Zhao, Dao-Xiu Zhou
Shoot-borne crown roots are the major root system in cereals. Previous work has shown that the Wuschel-related homeobox gene WOX11 is necessary and sufficient to promote rice (Oryza sativa) crown root emergence and elongation. Here, we show that WOX11 recruits the ADA2-GCN5 histone acetyltransferase (HAT) module to activate downstream target genes in crown root meristem. Rice ADA2 and GCN5 genes are highly expressed in root meristem and are shown to be essential for cell division and growth. WOX11 and ADA2-GCN5 commonly target and regulate a set of root-specific genes involved in energy metabolism, cell wall biosynthesis, and hormone response, some of which are known to be important for root development...
May 9, 2017: Plant Cell
https://www.readbyqxmd.com/read/28486630/paired-related-homeobox-1-transactivates-dopamine-d2-receptor-to-maintain-propagation-and-tumorigenicity-of-glioma-initiating-cells
#9
Yamu Li, Wen Wang, Fangyu Wang, Qiushuang Wu, Wei Li, Xiaoling Zhong, Kuan Tian, Tao Zeng, Liang Gao, Ying Liu, Shu Li, Xiaobing Jiang, Guangwei Du, Yan Zhou
Glioblastoma multiforme (GBM) is a highly invasive brain tumor with limited therapeutic means and poor prognosis. Recent studies indicate that glioma-initiating cells/glioma stem cells (GICs/GSCs) may be responsible for tumor initiation, infiltration, and recurrence. GICs could aberrantly employ molecular machinery balancing self-renewal and differentiation of embryonic neural precursors. Here, we find that paired related homeobox 1 (PRRX1), a homeodomain transcription factor that was previously reported to control skeletal development, is expressed in cortical neural progenitors and is required for their self-renewal and proper differentiation...
May 9, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28484484/over-expression-of-oshox24-confers-enhanced-susceptibility-to-abiotic-stresses-in-transgenic-rice-via-modulating-stress-responsive-gene-expression
#10
Annapurna Bhattacharjee, Raghvendra Sharma, Mukesh Jain
Homeobox transcription factors play critical roles in plant development and abiotic stress responses. In the present study, we raised rice transgenics over-expressing stress-responsive OsHOX24 gene (rice homeodomain-leucine zipper I sub-family member) and analyzed their response to various abiotic stresses at different stages of development. At the seed germination stage, rice transgenics over-expressing OsHOX24 exhibited enhanced sensitivity to abiotic stress conditions and abscisic acid as compared to wild-type (WT)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28474998/homeodomain-containing-gene-10-inhibits-cell-apoptosis-and-promotes-cell-invasion-and-migration-in-osteosarcoma-cell-lines
#11
Wen Xiong, Quan Zhou, Gang Liu, Xiang-Sheng Liu, Xin-Yu Li
Homeodomain-containing gene 10 (HOXC10) belongs to the homeobox family, which encodes a highly conserved family of transcription factors that plays an important role in morphogenesis in all multicellular organisms. Altered expressions of HOXC10 have been reported in several malignancies. This study was aimed to reveal the expression profile of HOXC10 in osteosarcoma and evaluated whether HOXC10 is a molecular target for cancer therapy. We found that HOXC10 was up-regulated in osteosarcoma tissues compared with bone cyst specimens from The Cancer Genome Atlas database...
May 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28473536/impact-of-cytosine-methylation-on-dna-binding-specificities-of-human-transcription-factors
#12
Yimeng Yin, Ekaterina Morgunova, Arttu Jolma, Eevi Kaasinen, Biswajyoti Sahu, Syed Khund-Sayeed, Pratyush K Das, Teemu Kivioja, Kashyap Dave, Fan Zhong, Kazuhiro R Nitta, Minna Taipale, Alexander Popov, Paul A Ginno, Silvia Domcke, Jian Yan, Dirk Schübeler, Charles Vinson, Jussi Taipale
The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family...
May 5, 2017: Science
https://www.readbyqxmd.com/read/28459454/conservation-and-innovation-in-the-dux4-family-gene-network
#13
Jennifer L Whiddon, Ashlee T Langford, Chao-Jen Wong, Jun Wen Zhong, Stephen J Tapscott
Facioscapulohumeral dystrophy (FSHD; MIM158900, MIM158901) is caused by misexpression of the DUX4 transcription factor in skeletal muscle. Animal models of FSHD are hindered by incomplete knowledge regarding the conservation of the DUX4 transcriptional program in other species. Despite the divergence of their binding motifs, both mouse DUX and human DUX4 in mouse and human muscle cells, respectively, activate genes associated with cleavage-stage embryos, including MERVL and ERVL-MaLR retrotransposons. We found that human DUX4 expressed in mouse cells maintained modest activation of cleavage-stage genes driven by conventional promoters but did not activate MERVL-promoted genes...
May 1, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28456934/lhx9-is-required-for-the-development-of-retinal-nitric-oxide-synthesizing-amacrine-cell-subtype
#14
Revathi Balasubramanian, Andrew Bui, Xuhui Dong, Lin Gan
Amacrine cells are the most diverse group of retinal neurons. Various subtypes of amacrine interneurons mediate a vast majority of image forming and non-image forming visual functions. The transcriptional regulation governing the development of individual amacrine cell subtypes is not well understood. One such amacrine cell subtype comprises neuronal nitric oxide synthase (nNOS/bNOS/NOS1)-expressing amacrine cells (NOACs) that regulate the release of nitric oxide (NO), a neurotransmitter with physiological and clinical implications in the retina...
April 29, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28455968/dishevelled-3-phosphorylation-is-governed-by-hipk2-pp1c%C3%AE-itch-axis-and-the-non-phosphorylated-form-promotes-cancer-stemness-via-lgr5-in-hepatocellular-carcinoma
#15
Yu-Man Tsui, Karen Man-Fong Sze, Edmund Kwok-Kwan Tung, Daniel Wai-Hung Ho, Terence Kin-Wah Lee, Irene Oi-Lin Ng
Dishevelled-3 (Dvl3) is regarded as a binding hub with many different interacting partners. However, its regulation and mechanism on cancer stemness remain to be explored. In this study, we showed that Dvl3 was significantly overexpressed in human hepatocellular carcinomas (HCCs) and promoted cancer stemness both in vitro and in vivo. We found that the non-phosphorylated (NP)-Dvl3 was more stable than the phosphorylated form, more active in activating β-catenin transcriptional activity, and more potent in enhancing self-renewal ability in HCC cells...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28455377/lmx1b-targeted-cis-regulatory-modules-involved-in-limb-dorsalization
#16
Endika Haro, Billy A Watson, Jennifer M Feenstra, Luke Tegeler, Charmaine U Pira, Subburaman Mohan, Kerby C Oberg
Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct gene targets in the limb have been confirmed. To determine direct targets, we performed a chromatin immunoprecipitation against Lmx1b at E12.5 followed by next generation sequencing (ChIP-seq). Nearly 84% (n=617) of the Lmx1b-bound genomic intervals (LBIs) identified overlap with chromatin regulatory marks indicative of potential cis-regulatory modules (PCRMs)...
April 28, 2017: Development
https://www.readbyqxmd.com/read/28450370/comparative-genomics-of-the-ectomycorrhizal-sister-species-rhizopogon-vinicolor-and-rhizopogon-vesiculosus-basidiomycota-boletales-reveals-a-divergence-of-the-mating-type-b-locus
#17
Alija Bajro Mujic, Alan Kuo, Andrew Tritt, Anna Lipzen, Cindy Chen, Jenifer Johnson, Aditi Sharma, Kerrie Barry, Igor V Grigoriev, Joseph W Spatafora
Divergence of breeding system plays an important role in fungal speciation. Ectomycorrhizal fungi, however, pose a challenge for the study of reproductive biology because most cannot be mated under laboratory conditions. To overcome this barrier, we sequenced the draft genomes of the ectomycorrhizal sister species Rhizopogon vinicolor Smith and Zeller and R. vesiculosus Smith and Zeller (Basidiomycota, Boletales), the first genomes available for Basidiomycota truffles, and characterized gene content and organization surrounding their mating type loci...
April 26, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28447749/dental-and-periodontal-phenotypes-of-dlx2-overexpression-in-mice
#18
Jiewen Dai, Jiawen Si, Ningjuan Ouyang, Jianfei Zhang, Dandan Wu, Xudong Wang, Guofang Shen
Distal-less homeobox 2 (Dlx2) is a member of the homeodomain family of transcription factors and is important for the development of cranial neural crest cells (CNCCs)‑derived craniofacial tissues. Previous studies revealed that Dlx2 was expressed in the cementum and a targeted null mutation disrupted tooth development in mice. However, whether Dlx2 overexpression may impair in vivo tooth morphogenesis remains to be elucidated. The present study used a transgenic mouse model to specifically overexpress Dlx2 in neural crest cells in order to identify the dental phenotypes in mice by observation, micro‑computed tomography and histological examination...
May 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28446706/a-sister-of-nanog-regulates-genes-expressed-in-pre-implantation-human-development
#19
Thomas L Dunwell, Peter W H Holland
The NANOG homeobox gene plays a pivotal role in self-renewal and maintenance of pluripotency in human, mouse and other vertebrate embryonic stem cells, and in pluripotent cells of the blastocyst inner cell mass. There is a poorly studied and atypical homeobox locus close to the Nanog gene in some mammals which could conceivably be a cryptic paralogue of NANOG, even though the loci share only 20% homeodomain identity. Here we argue that this gene, NANOGNB (NANOG Neighbour), is an extremely divergent duplicate of NANOG that underwent radical sequence change in the mammalian lineage...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28436679/cited2-mutations-in-conserved-regions-contribute-to-conotruncal-heart-defects-in-chinese-children
#20
Bojian Li, Tian Pu, Yang Liu, Yuejuan Xu, Rang Xu
Conotruncal heart defects (CTDs) are severe malformations of outflow tract with heterogeneous morphology. Several missense variants of CITED2 have been identified to cause CTDs in recent researches. In this study, we screened the coding regions of CITED2 in 605 Chinese children with CTDs and found two possible pathogenic mutant sites: p.Q117L and p.T257A, both located in the conserved regions of CITED2. Then, we investigated the biological and functional alterations of them. Western blotting showed low level of protein expression of mutant Q117 and T257A compared with wild-type CITED2...
April 24, 2017: DNA and Cell Biology
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