Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage

DE Goszczynski, MM Halstead, AD Islas-Trejo… - Genome …, 2021 - genome.cshlp.org
… By evaluating the chromatin landscape surrounding TSCs, we observed a consistent co-…
bp and were sequenced on an Illumina HiSeq 4000 system, generating paired-end reads of …

The landscape of promoter-centred RNA–DNA interactions in rice

Q Xiao, X Huang, Y Zhang, W Xu, Y Yang, Q Zhang… - Nature Plants, 2022 - nature.com
transcribed DNA strand, resulting in high enrichment of sense RNAs downstream of transcription
start … PCR products were then subjected to size selection and paired-end sequencing (2 …

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma

WF Ooi, AM Nargund, KJ Lim, S Zhang, M Xing… - Gut, 2020 - gut.bmj.com
… Of these tumour-associated enhancer-based SVs, 20% (n=30) exhibited breakpoints localised
at H3K27ac-enriched promoter regions (±2.5 Kb from annotated transcription start sites (…

[HTML][HTML] Mapping the genetic landscape of DNA double-strand break repair

JA Hussmann, J Ling, P Ravisankar, J Yan… - Cell, 2021 - cell.com
… damage across diverse pools of perturbed cells, followed by linked recovery of perturbation
identities and repair outcomes from individual cells by paired-end sequencing (Figure 1B). …

Defining genome architecture at base-pair resolution

P Hua, M Badat, LLP Hanssen, LD Hentges, N Crump… - Nature, 2021 - nature.com
… Fourth, we generated contact maps with base-pair accuracy by directly sequencing the …
paired-end sequencing by sonicating the MNase 3C library to 200-bp fragments and sequencing

Nascent RNA analyses: tracking transcription and its regulation

EM Wissink, A Vihervaara, ND Tippens… - Nature Reviews …, 2019 - nature.com
… With paired-end sequencing, these short, capped RNAs provide high-resolution … maps
of transcription initiation at putative enhancers obtained with GRO-cap, PRO-cap, and Start-seq …

The landscape of RNA Pol II binding reveals a stepwise transition during ZGA

B Liu, Q Xu, Q Wang, S Feng, F Lai, P Wang, F Zheng… - Nature, 2020 - nature.com
… with sequencing (Stacc–seq), we investigated the landscapes of … TSS, transcription start site.
b, UCSC browser views and heat … For paired-end reads, SNP information from both reads in …

[HTML][HTML] The landscape of transcription initiation across latent and lytic KSHV genomes

X Ye, Y Zhao, J Karijolich - PLoS Pathogens, 2019 - journals.plos.org
… Having mapped the transcription initiation landscape of PEL cells, we intersected FAIRE-seq
and CTCF chromatin immunoprecipitation sequencing (ChIP-seq) data sets with the …

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

C Zhu, M Yu, H Huang, I Juric, A Abnousi… - Nature structural & …, 2019 - nature.com
… the transcriptome and open chromatin landscapes in the major cell … around transcription start
sites (TSSs) and transcription … bwa mem’ to map the two ends of one paired-end read to the …

RNA polymerase II dynamics shape enhancer–promoter interactions

G Barshad, JJ Lewis, AG Chivu, A Abuhashem… - Nature …, 2023 - nature.com
… Hi-C\Micro-C unique paired-end reads (which we will refer to … Samples were paired-end
sequenced (read length = 150 bp) … define the position of transcription initiation at each of these …