scholarly journals Nitrogen cost minimization is promoted by structural changes in the transcriptome of N deprived Prochlorococcus cells

2016 ◽  
Author(s):  
Robert W. Read ◽  
Paul M. Berube ◽  
Steven J. Biller ◽  
Iva Neveux ◽  
Andres Cubillos-Ruiz ◽  
...  
Keyword(s):  
Structural Changes ◽  
Cost Minimization ◽  
Nutrient Requirements ◽  
Transcription Start ◽  
Marine Cyanobacterium ◽  
Transcription Start Sites ◽  
N Limitation ◽  
Genomic Adaptation ◽  
Slow Growing ◽  
Structure Of Proteins

AbstractProchlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might be used to further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions. Of 64 genes with primary and internal TSSs in both conditions, N-deprived cells initiated transcription downstream of primary TSSs more frequently than N-replete cells. Additionally, 117 genes with only an internal TSS demonstrated increased internal transcription under N-deprivation. These shortened transcripts encode predicted proteins with ~5-20% less N content compared to full-length transcripts. We hypothesized that low translation rates, which afford greater control over protein abundances, would be beneficial to relatively slow-growing organisms like Prochlorococcus. Consistent with this idea, we found that Prochlorococcus exhibits greater usage of glycine-glycine motifs, which cause translational pausing, when compared to faster growing microbes. Our findings indicate that structural changes occur within the Prochlorococcus MED4 transcriptome during N-deprivation, potentially altering the size and structure of proteins expressed under nutrient limitation.

scholarly journals Crystal structures of heterotypic nucleosomes containing histones H2A.Z and H2A

Open Biology ◽  
2016 ◽  
Vol 6 (6) ◽  
pp. 160127 ◽  
Author(s):  
Naoki Horikoshi ◽  
Yasuhiro Arimura ◽  
Hiroyuki Taguchi ◽  
Hitoshi Kurumizaka
Keyword(s):  
Crystal Structures ◽  
Essential Role ◽  
Structural Changes ◽  
Loop Structure ◽  
Transcription Start ◽  
Steric Clash ◽  
Transcription Start Sites ◽  
Nucleosome Structure ◽  
Loop Region ◽  
Epigenetic Regulator

H2A.Z is incorporated into nucleosomes located around transcription start sites and functions as an epigenetic regulator for the transcription of certain genes. During transcriptional regulation, the heterotypic H2A.Z/H2A nucleosome containing one each of H2A.Z and H2A is formed. However, previous homotypic H2A.Z nucleosome structures suggested that the L1 loop region of H2A.Z would sterically clash with the corresponding region of canonical H2A in the heterotypic nucleosome. To resolve this issue, we determined the crystal structures of heterotypic H2A.Z/H2A nucleosomes. In the H2A.Z/H2A nucleosome structure, the H2A.Z L1 loop structure was drastically altered without any structural changes of the canonical H2A L1 loop, thus avoiding the steric clash. Unexpectedly, the heterotypic H2A.Z/H2A nucleosome is more stable than the homotypic H2A.Z nucleosome. These data suggested that the flexible character of the H2A.Z L1 loop plays an essential role in forming the stable heterotypic H2A.Z/H2A nucleosome.

scholarly journals Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

PLoS ONE ◽  
2009 ◽  
Vol 4 (10) ◽  
pp. e7526 ◽  
Author(s):  
Alfredo Mendoza-Vargas ◽  
Leticia Olvera ◽  
Maricela Olvera ◽  
Ricardo Grande ◽  
Leticia Vega-Alvarado ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
E Coli ◽  
Factor Binding ◽  
Genome Wide

Transcription shapes 3D chromatin organization by interacting with loop-extruding cohesin complexes

2022 ◽  
Author(s):  
Edward J Banigan ◽  
Wen Tang ◽  
Aafke A van den Berg ◽  
Roman R Stocsits ◽  
Gordana Wutz ◽  
...  
Keyword(s):  
Functional Organization ◽  
Regulatory Elements ◽  
General Shape ◽  
Transcription Start ◽  
Double Knockout ◽  
Transcription Start Sites ◽  
Contact Patterns ◽  
New Type ◽  
Active Transcription ◽  
Distal Regulatory Elements

Cohesin organizes mammalian interphase chromosomes by reeling chromatin fibers into dynamic loops (Banigan and Mirny, 2020; Davidson et al., 2019; Kim et al., 2019; Yatskevich et al., 2019). "Loop extrusion" is obstructed when cohesin encounters a properly oriented CTCF protein (Busslinger et al., 2017; de Wit et al., 2015; Fudenberg et al., 2016; Nora et al., 2017; Sanborn et al., 2015; Wutz et al., 2017), and recent work indicates that other factors, such as the replicative helicase MCM (Dequeker et al., 2020), can also act as barriers to loop extrusion. It has been proposed that transcription relocalizes (Busslinger et al., 2017; Glynn et al., 2004; Lengronne et al., 2004) or interferes with cohesin (Heinz et al., 2018; Jeppsson et al., 2020; Valton et al., 2021; S. Zhang et al., 2021), and that active transcription start sites function as cohesin loading sites (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), but how these effects, and transcription in general, shape chromatin is unknown. To determine whether transcription can modulate loop extrusion, we studied cells in which the primary extrusion barriers could be removed by CTCF depletion and cohesin's residence time and abundance on chromatin could be increased by Wapl knockout. We found evidence that transcription directly interacts with loop extrusion through a novel "moving barrier" mechanism, but not by loading cohesin at active promoters. Hi-C experiments showed intricate, cohesin-dependent genomic contact patterns near actively transcribed genes, and in CTCF-Wapl double knockout (DKO) cells (Busslinger et al., 2017), genomic contacts were enriched between sites of transcription-driven cohesin localization ("cohesin islands"). Similar patterns also emerged in polymer simulations in which transcribing RNA polymerases (RNAPs) acted as "moving barriers" by impeding, slowing, or pushing loop-extruding cohesins. The model predicts that cohesin does not load preferentially at promoters and instead accumulates at TSSs due to the barrier function of RNAPs. We tested this prediction by new ChIP-seq experiments, which revealed that the "cohesin loader" Nipbl (Ciosk et al., 2000) co-localizes with cohesin, but, unlike in previous reports (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), Nipbl did not accumulate at active promoters. We propose that RNAP acts as a new type of barrier to loop extrusion that, unlike CTCF, is not stationary in its precise genomic position, but is itself dynamically translocating and relocalizes cohesin along DNA. In this way, loop extrusion could enable translocating RNAPs to maintain contacts with distal regulatory elements, allowing transcriptional activity to shape genomic functional organization.

scholarly journals Expression of murine muscle-enriched A-type lamin-interacting protein (MLIP) is regulated by tissue-specific alternative transcription start sites

2018 ◽  
Vol 293 (51) ◽  
pp. 19761-19770
Author(s):  
Marie-Elodie Cattin ◽  
Shelley A. Deeke ◽  
Sarah A. Dick ◽  
Zachary J. A. Verret-Borsos ◽  
Gayashan Tennakoon ◽  
...  
Keyword(s):  
Transcription Start ◽  
Interacting Protein ◽  
Tissue Specific ◽  
Transcription Start Sites ◽  
Alternative Transcription ◽  
Specific Alternative

Genomic organization of the 5′ end of human β-ENaC and preliminary characterization of its promoter

2002 ◽  
Vol 282 (5) ◽  
pp. F898-F909 ◽  
Author(s):  
Christie P. Thomas ◽  
Randy W. Loftus ◽  
Kang Z. Liu ◽  
Omar A. Itani
Keyword(s):  
Genomic Organization ◽  
Human Kidney ◽  
Β Subunit ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Nuclear Extracts ◽  
Flanking Region ◽  
Rapid Amplification ◽  
Flanking Regions

The mRNA for the β-subunit of the epithelial Na+ channel (β-ENaC) is regulated developmentally and, in some tissues, in response to corticosteroids. To understand the mechanisms of transcriptional regulation of the human β-ENaC gene, we characterized the 5′ end of the gene and its 5′-flanking regions. Adaptor-ligated human kidney and lung cDNA were amplified by 5′ rapid amplification of cDNA ends, and transcription start sites of two 5′ variant transcripts were determined by nuclease protection or primer extension assays. Cosmid clones that contain the 5′ end of the gene were isolated, and analysis of these clones indicated that alternate first exons ∼1.5 kb apart and ∼ 45 kb upstream of a common second exon formed the basis of these transcripts. Genomic fragments that included the proximal 5′-flanking region of either transcript were able to direct expression of a reporter gene in lung epithelia and to bind Sp1 in nuclear extracts, confirming the presence of separate promoters that regulate β-ENaC expression.

scholarly journals Opine-Based Agrobacterium Competitiveness: Dual Expression Control of the Agrocinopine Catabolism (acc) Operon by Agrocinopines and Phosphate Levels

2008 ◽  
Vol 190 (10) ◽  
pp. 3700-3711 ◽  
Author(s):  
H. Stanley Kim ◽  
Hyojeong Yi ◽  
Jaehee Myung ◽  
Kevin R. Piper ◽  
Stephen K. Farrand
Keyword(s):  
Plant Cells ◽  
Regulatory System ◽  
Food Sources ◽  
Competitive Environment ◽  
Operon Structure ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Expression Control ◽  
Maximum Utilization ◽  
Dual Expression

ABSTRACT Agrobacterium tumefaciens strain C58 can transform plant cells to produce and secrete the sugar-phosphate conjugate opines agrocinopines A and B. The bacterium then moves in response to the opines and utilizes them as exclusive sources of carbon, energy, and phosphate via the functions encoded by the acc operon. These privileged opine-involved activities contribute to the formation of agrobacterial niches in the environment. We found that the expression of the acc operon is induced by agrocinopines and also by limitation of phosphate. The main promoter is present in front of the first gene, accR, which codes for a repressor. This operon structure enables efficient repression when opine levels are low. The promoter contains two putative operators, one overlapping the −10 sequence and the other in the further upstream from it; two partly overlapped putative pho boxes between the two operators; and two consecutive transcription start sites. DNA fragments containing either of the operators bound purified repressor AccR in the absence of agrocinopines but not in the presence of the opines, demonstrating the on-off switch of the promoter. Induction of the acc operon can occur under low-phosphate conditions in the absence of agrocinopines and further increases when the opines also are present. Such opine-phosphate dual regulatory system of the operon may ensure maximum utilization of agrocinopines when available and thereby increase the chances of agrobacterial survival in the highly competitive environment with limited general food sources.

scholarly journals PREDICTION OF TRANSCRIPTION START SITES BASED ON FEATURE SELECTION USING AMOSA

2007 ◽  
Author(s):  
Xi Wang ◽  
Sanghamitra Bandyopadhya ◽  
Zhenyu Xuan ◽  
Xiaoyue Zhao ◽  
Michael Q. Zhang ◽  
...  
Keyword(s):  
Feature Selection ◽  
Transcription Start ◽  
Transcription Start Sites
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