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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...specific genomic sequences while interacting with regulatory proteins, RNA polymerase II, and the chromatin environment to direct gene expression programs. The set of expressed TFs and their activity in a cell determines which genes are expressed and to what level, thereby dictating cellular fate...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...-expressed genes suggests a contribution from post-transcriptional regulatory mechanisms. In C. elegans, diverse small RNA pathways are key post-transcriptional mediators of gene regulation, especially in the germline. These germline small RNA pathways typically affect transcript stability, but some have also been...
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Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
...most genes in C. elegans are trans-spliced to a 22-nt leader RNA (Blumenthal 2012), leading to removal and degradation of the initial 5′ sequence between the promoter and the trans-splice site, the beginning of the mature mRNA does not usually correspond to the transcription initiation site. Therefore...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...-level assembly of P. picta with whole- bisulfite sequencing and RNA-seq data, we determine that the YY1 transcription factor (YY1) DNA binding motif is associated with male-specific hypomethylated regions on the X, but not the autosomes. These YY1 motifs are the result of a recent and rapid repetitive element...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...polyadenylation site.For 5′ end filtering criterion (step 3 above), we implemented a stringent 5′ filtering step that kept reads if their 5′ ends fell within −100 to +15 of an annotated transcription start site or were supported by 5′ SAGE data or high-throughput sequencing of RNA polymerase II initiation sites...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...structures -wide in embryos and starved L1 larvae of the nematode Caenorhabditis elegans.Studies before ours showed that actively transcribing RNA polymerase II (Pol II) is the primary source of DNA supercoils in eukaryotes (Teves and Henikoff 2014). To transcribe DNA, Pol II and its nascent RNA must rotate...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...(Wahl et al. 2009). Global short-read sequencing (RNA-seq) of nascent RNA from yeast to human has revealed that most introns are removed from pre-mRNA during transcription by RNA polymerase II (Pol II) (Brugiolo et al. 2013). Therefore, spliceosome assembly and splicing occur on nascent RNA...
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Method: 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
...with ATF3 (Chu et al. 1994). TAF1 is an effector for pairs CTCF-TF, E2F1-TF, GABPA-TF, and MAX-TF (Table 1). Transcription initiation factor TFIID subunit 1, TAF1, appears in this global effector list, as the initiation of transcription by RNA polymerase II requires the coordination of TFIID...
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Research: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
- Amit Blumberg,
- Edward J. Rice,
- Anshul Kundaje,
- Charles G. Danko,
- and Dan Mishmar
Genome Res. March 2017 27: 362-373; Published in Advance January 3, 2017, doi:10.1101/gr.209924.116
...deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TISs) in the heavy and light strands revealed a novel conserved transcription...

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