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TranscriptomicsNascent elongating transcript sequencing (NET-seq) for Escherichia coli and Bacillus subtilis reveals a consensus pause sequence enriched at translation start sites.
Transcription by RNA polymerase (RNAP) is interrupted by pauses that play diverse regulatory roles. Although individual pauses have been studied in vitro, the determinants of pauses in vivo and their distribution throughout the bacterial genome remain unknown. Using nascent transcript sequencing we ...
ORGANISM(S): Bacillus subtilis 
2014-05-05 | E-GEOD-56720 | biostudies-arrayexpress
TranscriptomicsE2F in vivo binding specificity: comparison of consensus vs. non-consensus binding sites
Recent genome-scale ChIP-chip studies of transcription factors have shown that a low percentage of experimentally determined binding sites contain the consensus motif for the immunoprecipitated factor. In most cases, differences between in vivo target sites that contain or lack a consensus motif ha...
ORGANISM(S): Mus musculus 
2008-10-01 | E-GEOD-12126 | biostudies-arrayexpress
GenomicsExpanding the CTD code: methylation of non-consensus Lysine residues marks early transcription in mammalian cells
Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and co-transcriptional processing of nascent RNA. Extensive phosphorylation of serine residues occurs at the structurally-disorde...
ORGANISM(S): Mus musculus 
2015-12-22 | E-GEOD-72876 | biostudies-arrayexpress
GenomicsDNA specificity determinants associate with distinct transcription factor functions
To elucidate how genomic sequences build transcriptional control networks we need to understand the connection between DNA sequence and transcription factor binding and function. Binding predictions based solely on consensus predictions are limited because a single factor can use degenerate sequenc...
ORGANISM(S): Homo sapiens 
2009-12-18 | E-GEOD-17954 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human LNCaP cells to investigate androgen receptor mediated gene expression by a sequence-specific DNA binding polyamide
Androgen Receptor (AR) is essential for the growth and progression of prostate cancer in both hormone-sensitive and hormone-refractory disease. We have designed a sequence-specific DNA binding polyamide (1) that targets the consensus androgen response element (ARE). This polyamide binds the PSA pr...
ORGANISM(S): Homo sapiens 
2009-04-23 | E-GEOD-7708 | biostudies-arrayexpress
TranscriptomicsA modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity
We examine the use of high-throughput sequencing on binding sites recovered using a bacterial one-hybrid (B1H) system and find that improved models of transcription factor (TF) binding specificity can be obtained compared to standard methods of sequencing a small subset of the selected clones. We ca...
ORGANISM(S): synthetic construct 
2011-04-28 | E-GEOD-26767 | biostudies-arrayexpress
TranscriptomicsWidespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity
Transfected siRNAs and miRNAs regulate numerous transcripts that have only limited complementarity to the active strand of the RNA duplex. This process reflects natural target regulation by miRNAs, but is an unintended (â??off-targetâ??) consequence of siRNA-mediated silencing. Here we demonstrate...
ORGANISM(S): Homo sapiens 
2006-09-12 | E-GEOD-5814 | biostudies-arrayexpress
ProteomicsA sequence-specific RNA acetylation catalyst
N4-acetylcytidine (ac4C) is a ubiquitous RNA modification incorporated by cytidine acetyltransferase enzymes. Here, we report the biochemical characterization of Thermococcus kodakarensis Nat10 (TkNat10), an RNA acetyltransferase involved in archaeal thermotolerance. We demonstrate that TkNat10's ca...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2024-10-14 | MSV000096084 | MassIVE
GenomicsUnraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs
Short nascent strands purification coupled to next-generation sequencing allowed us to identify replication origins on human genome in an extensive way, by mapping replication origins in 4 different cell types, IMR-90 fibroblasts, hESC H9 cells, iPSC Th Cl-4 cells and HeLa cells. We demonstrated the...
ORGANISM(S): Homo sapiens 
2012-07-01 | E-GEOD-37757 | biostudies-arrayexpress
GenomicsMPXV consensus sequence data produce by the VEO taskforce from public INSDC data
Consensus sequences produced by VEO MPXV Taskforce
PRJEB55824 | ENA
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