Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

…, H Kawamoto, L M. Khachigian, SP Klinken, S Kojima… - Science, 2015 - science.org
Although it is generally accepted that cellular differentiation requires changes to transcriptional
networks, dynamic regulation of promoters and enhancers at specific sets of genes has …

CAGE: cap analysis of gene expression

R Kodzius, M Kojima, H Nishiyori, M Nakamura… - Nature …, 2006 - nature.com
Transcript abundance can be determined by various methods, including reverse transcription
(RT)-PCR, microarray analysis, sequencing of expressed sequence tags (ESTs), serial …

[HTML][HTML] FANTOM5 CAGE profiles of human and mouse samples

…, M Kanamori-Katayama, T Kawashima, M Kojima… - Scientific data, 2017 - nature.com
In the FANTOM5 project, transcription initiation events across the human and mouse genomes
were mapped at a single base-pair resolution and their frequencies were monitored by …

Unamplified cap analysis of gene expression on a single-molecule sequencer

…, H Kawaji, T Lassmann, S Katayama, M Kojima… - Genome …, 2011 - genome.cshlp.org
We report the development of a simplified cap analysis of gene expression (CAGE) protocol
adapted for single-molecule sequencers that avoids second strand synthesis, ligation, …

Functional annotation of human long noncoding RNAs via molecular phenotyping

…, H Kawaji, T Kawashima, ST Kelly, M Kojima… - Genome …, 2020 - genome.cshlp.org
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian
genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we …

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

…, AJ Knox, M Kojima, S Kojima… - Proceedings of the …, 2014 - National Acad Sciences
Naturally occurring regulatory T (Treg) cells, which specifically express the transcription
factor forkhead box P3 (Foxp3), are engaged in the maintenance of immunological self-…

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

…, G Pascarella, A Chalk, N Maeda, M Kojima… - Genome …, 2009 - genome.cshlp.org
Finding and characterizing mRNAs, their transcription start sites (TSS), and their associated
promoters is a major focus in post-genome biology. Mammalian cells have at least 5–10 …

Randomized, multicenter, comparative study of NEURO versus CIMT in poststroke patients with upper limb hemiparesis: the NEURO-VERIFY Study

…, R Momosaki, H Harashima, M Kojima… - … Journal of Stroke, 2014 - journals.sagepub.com
Background Many poststroke patients suffer functional motor limitation of the affected upper
limb, which is associated with diminished health-related quality of life. Aims The aim of this …

Simple fabrication of honeycomb-and pincushion-structured films containing thermoresponsive polymers and their surface wettability

H Yabu, Y Hirai, M Kojima, M Shimomura - Chemistry of Materials, 2009 - ACS Publications
Honeycomb- and pincushion-structured films with thermoresponsive functionalities were
fabricated by using the self-organization process. Amphiphilic copolymers with …

Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets

…, K Takano, A Higashida, M Kojima… - Journal of the …, 2023 - ACS Publications
Establishing a technological platform for creating clinical compounds inhibiting intracellular
protein–protein interactions (PPIs) can open the door to many valuable drugs. Although …