Volume 31, Issue 6 | June 2021

Research
- - Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy
    David W. Radke
    Jae Hoon Sul
    Daniel J. Balick
    Sebastian Akle
    Robert C. Green
    First Published May 7, 2021
  - Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
    Jia Huang
    Wenjun Chen
    Fan Zhou
    Zhichang Pang
    Luoluo Wang
    First Published April 15, 2021
  - Identification and characterization of centromeric sequences in Xenopus laevis
    Owen K. Smith
    Charles Limouse
    Kelsey A. Fryer
    Nicole A. Teran
    Kousik Sundararajan
    First Published April 19, 2021
  - CTCF looping is established during gastrulation in medaka embryos
    Ryohei Nakamura
    Yuichi Motai
    Masahiko Kumagai
    Candice L. Wike
    Haruyo Nishiyama
    Yoichiro Nakatani Neva C. Durand Kaori Kondo Takashi Kondo Tatsuya Tsukahara Atsuko Shimada
    ...[+6 authors]...,
    Bradley R. Cairns
    Erez Lieberman Aiden
    Shinichi Morishita
    Hiroyuki Takeda
    First Published May 18, 2021
  - Chromatin architecture transitions from zebrafish sperm through early embryogenesis
    Candice L. Wike
    Yixuan Guo
    Mengyao Tan
    Ryohei Nakamura
    Dana Klatt Shaw
    Noelia Díaz Aneasha F. Whittaker-Tademy Neva C. Durand Erez Lieberman Aiden
    ...[+4 authors]...,
    Juan M. Vaquerizas
    David Grunwald
    Hiroyuki Takeda
    Bradley R. Cairns
    First Published May 18, 2021
  - Antisense RNAs during early vertebrate development are divided in groups with distinct features
    Sanjana Pillay
    Hazuki Takahashi
    Piero Carninci
    Aditi Kanhere
    First Published April 1, 2021
  - Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation
    Yi-Ru Li
    Hsiao Wen Lai
    Hsiao Han Huang
    Hsing-Chun Chen
    Sebastian D. Fugmann
    First Published April 15, 2021
  - The mode of expression divergence in Drosophila fat body is infection-specific
    Bryan A. Ramirez-Corona
    Stephanie Fruth
    Oluchi Ofoegbu
    Zeba Wunderlich
    First Published April 15, 2021
  - Linking the dynamics of chromatin occupancy and transcription with predictive models
    Trung Q. Tran
    Heather K. MacAlpine
    Vinay Tripuraneni
    Sneha Mitra
    David M. MacAlpine
    First Published April 23, 2021
  - Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair
    Kaitlynne A. Bohm
    Amelia J. Hodges
    Wioletta Czaja
    Kathiresan Selvam
    Michael J. Smerdon
    First Published May 17, 2021
  - Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
    Kazumasa Shirai
    Mitsuhiko P. Sato
    Ranko Nishi
    Masahide Seki
    Yutaka Suzuki
    First Published May 18, 2021
Methods
- - Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories
    Alexandra Pokhilko
    Adam E. Handel
    Fabiola Curion
    Viola Volpato
    Emma S. Whiteley
    Sunniva Bøstrand Sarah E. Newey Colin J. Akerman
    ...[+3 authors]...,
    Caleb Webber
    Michael B. Clark
    Rory Bowden
    M. Zameel Cader
    First Published May 19, 2021
  - Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning
    Zeynep Kalender Atak
    Ibrahim Ihsan Taskiran
    Jonas Demeulemeester
    Christopher Flerin
    David Mauduit
    Liesbeth Minnoye Gert Hulselmans
    ...[+2 authors]...,
    Valerie Christiaens
    Ghanem-Elias Ghanem
    Jasper Wouters
    Stein Aerts
    First Published April 8, 2021
Resources
- - Modeling transcriptional regulation of model species with deep learning
    Evan M. Cofer
    João Raimundo
    Alicja Tadych
    Yuji Yamazaki
    Aaron K. Wong
    First Published April 22, 2021
  - Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring
    Kyu-Hyeon Yeom
    Zhicheng Pan
    Chia-Ho Lin
    Han Young Lim
    Wen Xiao
    First Published April 8, 2021

Table of Contents

Volume 31, Issue 6 | June 2021

Research

Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy

Tissue-specific reprogramming of host tRNA transcriptome by the microbiome

Identification and characterization of centromeric sequences in Xenopus laevis

CTCF looping is established during gastrulation in medaka embryos

Chromatin architecture transitions from zebrafish sperm through early embryogenesis

Antisense RNAs during early vertebrate development are divided in groups with distinct features

Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation

The mode of expression divergence in Drosophila fat body is infection-specific

Linking the dynamics of chromatin occupancy and transcription with predictive models

Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair

Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants

Methods

Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories

Interpretation of allele-specific chromatin accessibility using cell state–aware deep learning

Resources

Modeling transcriptional regulation of model species with deep learning

Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring

Table of Contents

Volume 31, Issue 6 | June 2021

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Research

Methods

Resources