Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation

Plotgardener: cultivating precise multi-panel figures in R

(2022) Nicole E Kramer et al.   BIOINFORMATICS

Gene architecture directs splicing outcome in separate nuclear spatial regions

(2022) Luna Tammer et al.   MOLECULAR CELL

Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries

(2022) Samuel Hunter et al.   BMC GENOMICS

Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory

(2022) Marco Dombrowski et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

(2022) Brad T Sherman et al.   NUCLEIC ACIDS RESEARCH

The missing linker: emerging trends for H1 variant-specific functions

(2021) Laura Prendergast et al.   GENES & DEVELOPMENT

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Binding Dynamics of Disordered Linker Histone H1 with a Nucleosomal Particle

(2021) Hao Wu et al.   JOURNAL OF MOLECULAR BIOLOGY

The upstream 5′ splice site remains associated to the transcription machinery during intron synthesis

(2021) Yodfat Leader et al.   Nature Communications

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Roles and mechanisms of alternative splicing in cancer — implications for care

(2020) Sophie C. Bonnal et al.   Nature Reviews Clinical Oncology

Site-Specific Phosphorylation of Histone H1.4 Is Associated with Transcription Activation

(2020) Ankita Saha et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

H1 histones control the epigenetic landscape by local chromatin compaction

(2020) Michael A. Willcockson et al.   NATURE

Alternative Splicing and Transcription Elongation in Plants

(2019) Micaela A. Godoy Herz et al.   Frontiers in Plant Science

Histone H1.5 binds over splice sites in chromatin and regulates alternative splicing

(2019) Ohad Glaich et al.   NUCLEIC ACIDS RESEARCH

Matt: Unix tools for alternative splicing analysis

(2018) André Gohr et al.   BIOINFORMATICS

Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin

(2018) Tushar Murthy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast

(2017) Vahid Aslanzadeh et al.   GENOME RESEARCH

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

(2017) Lydia Herzel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone H1 depletion triggers an interferon response in cancer cells via activation of heterochromatic repeats

(2017) Andrea Izquierdo-Bouldstridge et al.   NUCLEIC ACIDS RESEARCH

Linker histone H1 and protein–protein interactions

(2016) Anna A. Kalashnikova et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Modulation of chromatin function through linker histone H1 variants

(2016) Andrzej Kowalski et al.   BIOLOGY OF THE CELL

Chromatin Control of Developmental Dynamics and Plasticity

(2016) Matteo Perino et al.   DEVELOPMENTAL CELL

The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity

(2016) C. M. Torres et al.   SCIENCE

A Broad Set of Chromatin Factors Influences Splicing

(2016) Eric Allemand et al.   PLoS Genetics

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle

(2015) S. P. Hergeth et al.   EMBO REPORTS

Chromatin, DNA structure and alternative splicing

(2015) Nicolás Nieto Moreno et al.   FEBS LETTERS

Genome Distribution of Replication-independent Histone H1 Variants Shows H1.0 Associated with Nucleolar Domains and H1X Associated with RNA Polymerase II-enriched Regions

(2015) Regina Mayor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing

(2015) Silvia Jimeno-González et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells

(2015) Camilla Iannone et al.   RNA

The alternative role of DNA methylation in splicing regulation

(2015) Galit Lev Maor et al.   TRENDS IN GENETICS

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

Citrullination regulates pluripotency and histone H1 binding to chromatin

(2014) Maria A. Christophorou et al.   NATURE

Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2

(2014) Lluís Millán-Ariño et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

RNA Polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation

(2014) Elizabeth A Bowman et al.   Nucleus

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

Chromatin’s thread to alternative splicing regulation

(2013) Camilla Iannone et al.   CHROMOSOMA

Recombinant antibodies to histone post-translational modifications

(2013) Takamitsu Hattori et al.   NATURE METHODS

Target analysis by integration of transcriptome and ChIP-seq data with BETA

(2013) Su Wang et al.   Nature Protocols

Linker histone H1.0 interacts with an extensive network of proteins found in the nucleolus

(2013) Anna A. Kalashnikova et al.   NUCLEIC ACIDS RESEARCH

H1 histones: current perspectives and challenges

(2013) S. W. Harshman et al.   NUCLEIC ACIDS RESEARCH

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Linker Histone H1.2 Cooperates with Cul4A and PAF1 to Drive H4K31 Ubiquitylation-Mediated Transactivation

(2013) Kyunghwan Kim et al.   Cell Reports

The Genomic Landscape of the Somatic Linker Histone Subtypes H1.1 to H1.5 in Human Cells

(2013) Annalisa Izzo et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Alternative splicing: decoding an expansive regulatory layer

(2012) Manuel Irimia et al.   CURRENT OPINION IN CELL BIOLOGY

N- and C-terminal Domains Determine Differential Nucleosomal Binding Geometry and Affinity of Linker Histone Isotypes H10and H1c

(2012) Payal Vyas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functional interplay between p53 acetylation and H1.2 phosphorylation in p53-regulated transcription

(2012) K Kim et al.   ONCOGENE

Design principles of interconnections between chromatin and pre-mRNA splicing

(2012) Sérgio F. de Almeida et al.   TRENDS IN BIOCHEMICAL SCIENCES

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Dynamic Distribution of Linker Histone H1.5 in Cellular Differentiation

(2012) Jing-Yu Li et al.   PLoS Genetics

More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation

(2011) Reini F Luco et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

(2010) Satu Nahkuri et al.   CELL CYCLE

From chromatin to splicing: RNA-processing as a total artwork

(2010) Hagen Tilgner et al.   Epigenetics

Histone H1 phosphorylation is associated with transcription by RNA polymerases I and II

(2010) Yupeng Zheng et al.   JOURNAL OF CELL BIOLOGY

The organization of nucleosomes around splice sites

(2010) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Site-specifically phosphorylated forms of H1.5 and H1.2 localized at distinct regions of the nucleus are related to different processes during the cell cycle

(2009) Heribert Talasz et al.   CHROMOSOMA

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

When chromatin meets splicing

(2009) Alberto R Kornblihtt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The histone H1 family: specific members, specific functions?

(2008) Annalisa Izzo et al.   BIOLOGICAL CHEMISTRY

Alternative Splicing and Tumor Progression

(2008) Claudia Ghigna et al.   CURRENT GENOMICS

Histone H1 and its isoforms: Contribution to chromatin structure and function

(2008) Nicole Happel et al.   GENE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Depletion of Human Histone H1 Variants Uncovers Specific Roles in Gene Expression and Cell Growth

(2008) Mónica Sancho et al.   PLoS Genetics