Nascent RNA sequencing reveals distinct features in plant transcription (Q37379794)

20 August 2017

Nascent RNA sequencing reveals distinct features in plant transcription (English)

1 reference

20 August 2017

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

Chris Benner

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

4

Joanne Chory

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

author name string

Jonathan Hetzel

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

language of work or name

English

0 references

publication date

11 October 2016

1 reference

Proceedings of the National Academy of Sciences of the United States of America

20 August 2017

6

1 reference

based on heuristic

inferred from page(s)

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

volume

113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

issue

43

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

page(s)

12316-12321

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites.

2 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The Arabidopsis thaliana TCP transcription factors: A broadening horizon beyond development

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The core promoter: At the heart of gene expression.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Regulatory link between DNA methylation and active demethylation in Arabidopsis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Getting up to speed with transcription elongation by RNA polymerase II

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Evolution and diversification of the basal transcription machinery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Nascent transcription affected by RNA polymerase IV in Zea mays

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Human promoters are intrinsically directional

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

TRF2 and the evolution of the bilateria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Enhancer RNA facilitates NELF release from immediate early genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Determination and inference of eukaryotic transcription factor sequence specificity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Precise maps of RNA polymerase reveal how promoters direct initiation and pausing

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

STAR: ultrafast universal RNA-seq aligner

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Landscape of transcription in human cells

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

An integrated encyclopedia of DNA elements in the human genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

RNA polymerase II pausing downstream of core histone genes is different from genes producing polyadenylated transcripts

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Native elongating transcript sequencing (NET-seq).

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Fast gapped-read alignment with Bowtie 2

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Integrative genomics viewer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The NIH Roadmap Epigenomics Mapping Consortium

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Human DNA methylomes at base resolution show widespread epigenomic differences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Regulation of gene expression via the core promoter and the basal transcriptional machinery.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Divergent transcription: a new feature of active promoters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The antisense transcriptomes of human cells

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

RNA exosome depletion reveals transcription upstream of active human promoters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in Arabidopsis thaliana

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Genome wide analysis of Arabidopsis core promoters

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The RNA polymerase II core promoter

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Mechanism of transcription initiation and promoter escape by RNA polymerase II.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Relationship between nucleosome positioning and DNA methylation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Separation and partial characterization of three functional steps in transcription initiation by human RNA polymerase II.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Identification of TATA and TATA-less promoters in plant genomes by integrating diversity measure, GC-Skew and DNA geometric flexibility.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5087027

Heterogeneity of Arabidopsis core promoters revealed by high-density TSS analysis

2 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27729530

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1603217113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27729530 AND SRC:MED&resulttype=core&format=json

2 June 2020

PubMed publication ID

27729530

1 reference