Human promoters are intrinsically directional (Q35108213)

6 August 2017

Human promoters are intrinsically directional (English)

1 reference

6 August 2017

Mahmoud M Ibrahim

3

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Sascha H Duttke

object named as

Sascha H C Duttke

1

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Sven Heinz

object named as

Sven Heinz

7

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Uwe Ohler

9

object named as

Uwe Ohler

1 reference

6 August 2017

4

Christopher K Glass

1 reference

6 August 2017

Scott A Lacadie

2

1 reference

6 August 2017

David L Corcoran

5

1 reference

6 August 2017

Christopher Benner

6

1 reference

6 August 2017

James T Kadonaga

8

1 reference

6 August 2017

29 January 2015

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6 August 2017

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6 August 2017

57

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6 August 2017

4

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6 August 2017

674-684

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describes a project that uses

6 August 2017

1 reference

10 June 2022

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&rettype=xml&id=4336624

cites work

Terminate and make a loop: regulation of transcriptional directionality

1 reference

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RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro.

9 July 2018

1 reference

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An atlas of active enhancers across human cell types and tissues

9 July 2018

1 reference

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Divergent transcription is associated with promoters of transcriptional regulators

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Transcriptome surveillance by selective termination of noncoding RNA synthesis.

9 July 2018

1 reference

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Software for computing and annotating genomic ranges

9 July 2018

1 reference

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Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

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

9 July 2018

1 reference

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H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Defining the status of RNA polymerase at promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

The RNA polymerase II CTD coordinates transcription and RNA processing.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Predicting cell-type-specific gene expression from regions of open chromatin

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

The accessible chromatin landscape of the human genome

9 July 2018

1 reference

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An integrated encyclopedia of DNA elements in the human genome

9 July 2018

1 reference

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The UCSC genome browser and associated tools

9 July 2018

1 reference

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mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Histone methylation: a dynamic mark in health, disease and inheritance

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Fast gapped-read alignment with Bowtie 2

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

ChromHMM: automating chromatin-state discovery and characterization

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

The dual lives of bidirectional promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Genome-wide structure and organization of eukaryotic pre-initiation complexes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

A paired-end sequencing strategy to map the complex landscape of transcription initiation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

BEDTools: a flexible suite of utilities for comparing genomic features

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Divergent transcription: a new feature of active promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

A transcription factor affinity-based code for mammalian transcription initiation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Divergent transcription from active promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

RNA exosome depletion reveals transcription upstream of active human promoters

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

High-resolution mapping and characterization of open chromatin across the genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

A code for transcription initiation in mammalian genomes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

RNA maps reveal new RNA classes and a possible function for pervasive transcription

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Antisense transcription in the mammalian transcriptome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

The transcriptional landscape of the mammalian genome

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

ROCR: visualizing classifier performance in R

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

The RNA polymerase II core promoter: a key component in the regulation of gene expression

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

CpG islands in vertebrate genomes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

JAMM: a peak finder for joint analysis of NGS replicates

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

Bidirectional gene organization: a common architectural feature of the human genome.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4336624

10.1016/J.MOLCEL.2014.12.029

27 September 2018

Identifiers

DOI

1 reference

6 August 2017

1 reference

6 August 2017

1 reference