4.7 Article

Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Jaime A. Castro-Mondragon et al.

Summary: JASPAR is an open-access database containing manually curated, non-redundant transcription factor binding profiles across six taxonomic groups. The latest release introduces new profiles for plants, vertebrates, urochordates, and insects, as well as new tools for TFBS enrichment analysis and data access. The database can be accessed through various platforms, including the JASPAR website, RESTful API, R/Bioconductor data package, and a new Python package pyJASPAR.

NUCLEIC ACIDS RESEARCH (2022)

Review Cell Biology

Enhancer grammar in development, evolution, and disease: dependencies and interplay

Granton A. Jindal et al.

Summary: The text discusses how biologists study the grammatical rules related to enhancer sequences and gene expression by searching for principles governing their relationship, in order to decipher the instructions within genomes and identify potentially disease- and evolution-related enhancer variants.

DEVELOPMENTAL CELL (2021)

Article Biochemistry & Molecular Biology

A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells

Gurdeep Singh et al.

Summary: Transcriptional enhancers play a critical role in development and phenotype evolution, and a diverse repertoire of TFBS sequences is necessary for constructing synthetic enhancers with comparable activity to native enhancers. A threshold of TFBS sequence diversity overrides the need for optimized regulatory grammar and specific master regulators' recruitment by individual TFBSs. At least 10 different TFBSs are required for enhancer activity, with some specific TFBSs being dispensable.

GENOME RESEARCH (2021)

Article Biochemistry & Molecular Biology

A model of active transcription hubs that unifies the roles of active promoters and enhancers

Iris Zhu et al.

Summary: The study reveals that active promoters and enhancers often cluster together in a pattern where the number of enhancers decreases as the number of active promoters increases, and there are few distant enhancers in regions with multiple closely located active genes. Interactions among regulatory elements predominantly occur in clusters, and the distance preference between linearly close elements is approximately 30 kb.

NUCLEIC ACIDS RESEARCH (2021)

Review Biochemistry & Molecular Biology

Transcriptional enhancers and their communication with gene promoters

Helen Ray-Jones et al.

Summary: Transcriptional enhancers play a key role in regulating gene expression in metazoa, particularly in initiating and maintaining gene expression programmes. Understanding how enhancers control their target genes in the right place and time is a crucial question in functional genomics, and modern approaches are beginning to unravel the complexity of enhancer-promoter relationships.

CELLULAR AND MOLECULAR LIFE SCIENCES (2021)

Article Biochemistry & Molecular Biology

Enhancers with tissue-specific activity are enriched in intronic regions

Beatrice Borsari et al.

Summary: The study explored the correlation between the genomic location of active enhancers and tissue-specific gene expression, revealing that tissue-specific enhancers are enriched in intronic regions and control genes involved in tissue-specific functions. The results suggest that the genomic location of active enhancers is crucial for the tissue-specific control of gene expression, with the transition from developmental to adult stages showing a continuum of intergenic to intronic enhancers.

GENOME RESEARCH (2021)

Review Biotechnology & Applied Microbiology

Mechanisms of enhancer action: the known and the unknown

Anil Panigrahi et al.

Summary: Differential gene expression mechanisms and enhancers play crucial roles in cellular differentiation and diversity, yet our understanding of the detailed mechanics of enhancer action and the regulatory proteins involved remains incomplete.

GENOME BIOLOGY (2021)

Review Biochemistry & Molecular Biology

Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns

Divyanshi Srivastava et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2020)

Review Genetics & Heredity

Towards a comprehensive catalogue of validated and target-linked human enhancers

Molly Gasperini et al.

NATURE REVIEWS GENETICS (2020)

Review Biochemistry & Molecular Biology

Evaluating Enhancer Function and Transcription

Andrew Field et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 89 (2020)

Article Multidisciplinary Sciences

Global reference mapping of human transcription factor footprints

Jeff Vierstra et al.

NATURE (2020)

Article Multidisciplinary Sciences

Occupancy maps of 208 chromatin-associated proteins in one human cell type

E. Christopher Partridge et al.

NATURE (2020)

Article Multidisciplinary Sciences

Deep conservation of the enhancer regulatory code in animals

Emily S. Wong et al.

SCIENCE (2020)

Article Biochemistry & Molecular Biology

HOT or not: examining the basis of high-occupancy target regions

Katarzyna Wreczycka et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Biochemistry & Molecular Biology

The Human Transcription Factors

Samuel A. Lambert et al.

Article Cell & Tissue Engineering

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

Tahsin Stefan Barakat et al.

CELL STEM CELL (2018)

Article Multidisciplinary Sciences

Enhancer redundancy provides phenotypic robustness in mammalian development

Marco Osterwalder et al.

NATURE (2018)

Article Multidisciplinary Sciences

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

Bin Li et al.

SCIENTIFIC REPORTS (2017)

Article Biochemical Research Methods

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

Nathan C. Sheffield et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

Ge Tan et al.

BIOINFORMATICS (2016)

Review Biochemistry & Molecular Biology

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

Hannah K. Long et al.

Article Genetics & Heredity

Hierarchy within the mammary STAT5-driven Wap super-enhancer

Ha Youn Shin et al.

NATURE GENETICS (2016)

Article Genetics & Heredity

Genetic dissection of the α-globin super-enhancer in vivo

Deborah Hay et al.

NATURE GENETICS (2016)

Article Biochemistry & Molecular Biology

Enhancer Evolution across 20 Mammalian Species

Diego Villar et al.

Editorial Material Biochemistry & Molecular Biology

Enhancers: Holding Out for the Right Promoter

David S. Lorberbaum et al.

CURRENT BIOLOGY (2015)

Review Cell Biology

The selection and function of cell type-specific enhancers

Sven Heinz et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

Article Multidisciplinary Sciences

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation

Muhammad A. Zabidi et al.

NATURE (2015)

Article Multidisciplinary Sciences

An atlas of active enhancers across human cell types and tissues

Robin Andersson et al.

NATURE (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

Warren A. Whyte et al.

Article Biochemistry & Molecular Biology

Super-Enhancers in the Control of Cell Identity and Disease

Denes Hnisz et al.

Article Biochemistry & Molecular Biology

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

Jason Gertz et al.

MOLECULAR CELL (2013)

Review Genetics & Heredity

Human housekeeping genes, revisited

Eli Eisenberg et al.

TRENDS IN GENETICS (2013)

Article Biochemistry & Molecular Biology

Sequence and chromatin determinants of cell-type-specific transcription factor binding

Aaron Arvey et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Stephen G. Landt et al.

GENOME RESEARCH (2012)

Article Multidisciplinary Sciences

An expansive human regulatory lexicon encoded in transcription factor footprints

Shane Neph et al.

NATURE (2012)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Developmental Biology

Perspectives on the RNA polymerase II core promoter

James T. Kadonaga

WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY (2012)

Article Biochemical Research Methods

FIMO: scanning for occurrences of a given motif

Charles E. Grant et al.

BIOINFORMATICS (2011)

Article Multidisciplinary Sciences

Widespread transcription at neuronal activity-regulated enhancers

Tae-Kyung Kim et al.

NATURE (2010)

Article Genetics & Heredity

ChIP-Seq identification of weakly conserved heart enhancers

Matthew J. Blow et al.

NATURE GENETICS (2010)

Article Multidisciplinary Sciences

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Menno P. Creyghton et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Oncology

Cell line misidentification: the beginning of the end

John R. W. Masters

NATURE REVIEWS CANCER (2010)

Article Biochemical Research Methods

Comparative Proteomic Phenotyping of Cell Lines and Primary Cells to Assess Preservation of Cell Type-specific Functions

Cuiping Pan et al.

MOLECULAR & CELLULAR PROTEOMICS (2009)

Article Multidisciplinary Sciences

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Nathaniel D. Heintzman et al.

NATURE (2009)

Review Genetics & Heredity

Transcription factories: gene expression in unions?

Heidi Sutherland et al.

NATURE REVIEWS GENETICS (2009)

Article Biotechnology & Applied Microbiology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang et al.

GENOME BIOLOGY (2008)

Article Genetics & Heredity

The β-globin nuclear compartment in development and erythroid differentiation

RJ Palstra et al.

NATURE GENETICS (2003)