Table of Contents

Research

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Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
- Emily J. Collins,
- Mariana P. Cervantes-Silva,
- George A. Timmons,
- James R. O'Siorain,
- Annie M. Curtis,
- and Jennifer M. Hurley
Genome Res. February 2021 31: 171-185; Published in Advance January 12, 2021, doi:10.1101/gr.263814.120
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KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
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Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals
- Daniel W. Bellott and
- David C. Page
Genome Res. February 2021 31: 198-210; Published in Advance January 21, 2021, doi:10.1101/gr.268516.120
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Cis-acting variation is common across regulatory layers but is often buffered during embryonic development
- Swann Floc'hlay,
- Emily S. Wong,
- Bingqing Zhao,
- Rebecca R. Viales,
- Morgane Thomas-Chollier,
- Denis Thieffry,
- David A. Garfield,
- and Eileen E.M. Furlong
Genome Res. February 2021 31: 211-224; Published in Advance December 11, 2020, doi:10.1101/gr.266338.120
OPEN ACCESS ARTICLE
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Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
OPEN ACCESS ARTICLE
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Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity
- Alexander Crits-Christoph,
- Nicholas Bhattacharya,
- Matthew R. Olm,
- Yun S. Song,
- and Jillian F. Banfield
Genome Res. February 2021 31: 239-250; Published in Advance December 23, 2020, doi:10.1101/gr.268169.120
OPEN ACCESS ARTICLE

Methods

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TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
- Liguo Zhang,
- Yang Zhang,
- Yu Chen,
- Omid Gholamalamdari,
- Yuchuan Wang,
- Jian Ma,
- and Andrew S. Belmont
Genome Res. February 2021 31: 251-264; Published in Advance December 18, 2020, doi:10.1101/gr.266239.120
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Evidence of widespread, independent sequence signature for transcription factor cobinding
- Manqi Zhou,
- Hongyang Li,
- Xueqing Wang,
- and Yuanfang Guan
Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
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Epigenomic differences in the human and chimpanzee genomes are associated with structural variation
- Xiaoyu Zhuo,
- Alan Y. Du,
- Erica C. Pehrsson,
- Daofeng Li,
- and Ting Wang
Genome Res. February 2021 31: 279-290; Published in Advance December 10, 2020, doi:10.1101/gr.263491.120
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Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
- Zhiyi Sun,
- Romualdas Vaisvila,
- Laura-Madison Hussong,
- Bo Yan,
- Chloé Baum,
- Lana Saleh,
- Mala Samaranayake,
- Shengxi Guan,
- Nan Dai,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Theodore B. Davis,
- Thomas C. Evans, Jr.,
- and Laurence M. Ettwiller
Genome Res. February 2021 31: 291-300; Published in Advance January 19, 2021, doi:10.1101/gr.265306.120
OPEN ACCESS ARTICLE
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Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments
- Ales Varabyou,
- Steven L. Salzberg,
- and Mihaela Pertea
Genome Res. February 2021 31: 301-308; Published in Advance December 23, 2020, doi:10.1101/gr.266213.120
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Contamination detection in sequencing studies using the mitochondrial phylogeny
- Hansi Weissensteiner,
- Lukas Forer,
- Liane Fendt,
- Azin Kheirkhah,
- Antonio Salas,
- Florian Kronenberg,
- and Sebastian Schoenherr
Genome Res. February 2021 31: 309-316; Published in Advance January 15, 2021, doi:10.1101/gr.256545.119
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Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120

Resources

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A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
- Matthew D.C. Neville,
- Robin Kohze,
- Chaitanya Erady,
- Narendra Meena,
- Matthew Hayden,
- David N. Cooper,
- Matthew Mort,
- and Sudhakaran Prabakaran
Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
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Modeling molecular development of breast cancer in canine mammary tumors
- Kiley Graim,
- Dmitriy Gorenshteyn,
- David G. Robinson,
- Nicholas J. Carriero,
- James A. Cahill,
- Rumela Chakrabarti,
- Michael H. Goldschmidt,
- Amy C. Durham,
- Julien Funk,
- John D. Storey,
- Vessela N. Kristensen,
- Chandra L. Theesfeld,
- Karin U. Sorenmo,
- and Olga G. Troyanskaya
Genome Res. February 2021 31: 337-347; Published in Advance December 23, 2020, doi:10.1101/gr.256388.119
OPEN ACCESS ARTICLE

Research

Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states

KDM1A maintains genome-wide homeostasis of transcriptional enhancers

Dosage-sensitive functions in embryonic development drove the survival of genes on sex-specific chromosomes in snakes, birds, and mammals

Cis-acting variation is common across regulatory layers but is often buffered during embryonic development

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity

Methods

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

Evidence of widespread, independent sequence signature for transcription factor cobinding

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution

Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments

Contamination detection in sequencing studies using the mitochondrial phylogeny

Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics

Resources

A platform for curated products from novel open reading frames prompts reinterpretation of disease variants

Modeling molecular development of breast cancer in canine mammary tumors

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