Volume 35, Issue 6 | June 2025

Mini-Review
- - Revisiting models of enhancer–promoter communication in gene regulation
    Gilad Barshad
    Charles G. Danko
    First Published June 2, 2025
Research
- - Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
    Koichi Kitao
    Kenji Ichiyanagi
    So Nakagawa
    First Published May 8, 2025
  - Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
    Keegan S. Krick
    Marissa Maroni
    Erica Korb
    Kristen W. Lynch
    Elizabeth A. Heller
    First Published April 24, 2025
  - Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
    Yu-Chi Chen
    David L.J. Vendrami
    Maximilian L. Huber
    Luisa E.Y. Handel
    Christopher R. Cooney
    First Published March 31, 2025
  - Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
    Siyu Xie
    Jun Li
    Wanyan Chen
    Lydia J.M. Fong
    Chunhua Huang
    Yan Feng
    ...[+1 authors]...,
    Qingbo Ai
    Mian Zhao
    Judith E. Mank
    Hua Wu
    First Published April 24, 2025
  - Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
    Marcus J. Viscardi
    Enisha Sehgal
    Joshua A. Arribere
    First Published May 9, 2025
  - Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
    Chenbo Gong
    Yicheng Huang
    Mengmeng Liu
    Yong Zhou
    Yinwei Xu
    Nahed Mohammed Xintong Qiao Andrea Zuccolo Weibo Xie
    ...[+4 authors]...,
    Rod A. Wing
    Jianwei Zhang
    Fei Zhou
    Yongjun Lin
    First Published April 25, 2025
  - Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
    Rita Tam
    Mareike Möller
    Runpeng Luo
    Zhenyan Luo
    Ashley Jones
    First Published April 11, 2025
  - Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
    Abigail L. Lind
    Nathan A. McDonald
    Elias R. Gerrick
    Ami S. Bhatt
    Katherine S. Pollard
    First Published April 22, 2025
Methods
- - Analytical validation of germline small variant detection using long-read HiFi genome sequencing
    Nathan Hammond
    Linda Liao
    Pun Wai Tong
    Zena Ng
    Thuy-Mi P. Nguyen
    First Published April 11, 2025
  - Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data
    Lulu Yan
    Jinyu Cheng
    Qing Nie
    Xiaoqiang Sun
    First Published April 22, 2025
  - STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
    Congcong Hu
    Nana Wei
    Jiyuan Yang
    Hua-Jun Wu
    Xiaoqi Zheng
    First Published May 12, 2025
  - TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data
    Chen Li
    Sijie Chen
    Yixin Chen
    Haiyang Bian
    Minsheng Hao
    First Published April 10, 2025
  - Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    Paras Verma
    Deeksha Thakur
    Deepanshi Awasthi
    Shashi Bhushan Pandit
    First Published May 7, 2025
Resource
- - Charting the regulatory landscape of TP53 on transposable elements in cancer
    Xuan Qu
    Yonghao Liang
    Colin McCornack
    Xiaoyun Xing
    Heather Schmidt
    Chad Tomlinson
    ...[+1 authors]...,
    Catrina Fronick
    Edward A. Belter
    Juan F. Macias-Velasco
    Ting Wang
    First Published May 13, 2025
Corrigenda
- - Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
    Jonathan Cahn
    James P.B. Lloyd
    Ino D. Karemaker
    Pascal W.T.C. Jansen
    Jahnvi Pflueger
    Owen Duncan Jakob Petereit
    ...[+2 authors]...,
    Ozren Bogdanovic
    A. Harvey Millar
    Michiel Vermeulen
    Ryan Lister
    First Published June 2, 2025
  - Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing
    Kepin Wang
    Qin Jin
    Degong Ruan
    Yi Yang
    Qishuai Liu
    Han Wu Zhiwei Zhou Zhen Ouyang Zhaoming Liu Yu Zhao Bentian Zhao Quanjun Zhang Jiangyun Peng Chengdan Lai Nana Fan Yanhui Liang Ting Lan Nan Li Xiaoshan Wang Xinlu Wang Yong Fan Pieter A. Doevendans
    ...[+17 authors]...,
    Joost P.G. Sluijter
    Pentao Liu
    Xiaoping Li
    Liangxue Lai
    First Published June 2, 2025

Table of Contents

Volume 35, Issue 6 | June 2025

Mini-Review

Revisiting models of enhancer–promoter communication in gene regulation

Research

Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon

Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing

Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes

Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad

Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay

Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza

Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus

Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology

Methods

Analytical validation of germline small variant detection using long-read HiFi genome sequencing

Dissecting multilayer cell–cell communications with signaling feedback loops from spatial transcriptomics data

STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data

TFcomb identifies transcription factor combinations for cellular reprogramming based on single-cell multiomics data

Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes

Resource

Charting the regulatory landscape of TP53 on transposable elements in cancer

Corrigenda

Corrigendum: Characterization of DNA methylation reader proteins in Arabidopsis thaliana

Corrigendum: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing

Table of Contents

Volume 35, Issue 6 | June 2025

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Mini-Review

Research

Methods

Resource

Corrigenda