diff --git a/NEWS.md b/NEWS.md
index a00e65c..795e813 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -21,6 +21,9 @@ NEW FEATURES
 -   Accelerated the computation of quantile position by ~20 times.
 -   New `resetCAGEexp()` function.
 -   New `flagByUpstreamSequences()` function.
+-   The `annotateCTSS` and `annotateConsensusClusters` function gain a
+    `upstream` and a `downstream` parameter to change the width of promoter
+    regions.
 
 # Changes in version 2.6.0
 
diff --git a/R/Annotations.R b/R/Annotations.R
index b13b4e4..0dfce0a 100644
--- a/R/Annotations.R
+++ b/R/Annotations.R
@@ -374,17 +374,21 @@ msScope_annotation <- function(libs) {
 }
 
 
-#' @name annotateCTSS
+#' Annotate and compute summary statistics
 #' 
-#' @title Annotate and compute summary statistics
-#' 
-#' @description `annotateCTSS` annotates the _CTSS_ of a [`CAGEexp`] object and
-#' computes annotation statistics.
+#' `annotateCTSS` annotates the _CTSS_ of a [`CAGEexp`] object and computes
+#' annotation statistics.
 #' 
 #' @param object `CAGEexp` object.
 #'   
 #' @param ranges A [`GRanges`] object, optionally containing `gene_name`,
 #'   `type` and `transcript_type` metadata.
+#' 
+#' @param upstream Number of bases _upstream_ the start of the transcript models
+#'        to be considered as part of the _promoter region_.
+#'        
+#' @param downstream Number of bases _downstream_ the start of the transcript
+#'        models to be considered as part of the _promoter region_.
 #'   
 #' @return `annotateCTSS` returns the input object with the following
 #'   modifications:
@@ -411,13 +415,14 @@ msScope_annotation <- function(libs) {
 #' 
 #' @export
 
-setGeneric("annotateCTSS", function(object, ranges) standardGeneric("annotateCTSS"))
+setGeneric("annotateCTSS", function(object, ranges, upstream=500, downstream=500)
+  standardGeneric("annotateCTSS"))
 
 #' @rdname annotateCTSS
 
-setMethod("annotateCTSS", c("CAGEexp", "GRanges"), function (object, ranges){
+setMethod("annotateCTSS", c("CAGEexp", "GRanges"), function (object, ranges, upstream=500, downstream=500){
   CTSScoordinatesGR(object)$genes      <- ranges2genes(CTSScoordinatesGR(object), ranges)
-  CTSScoordinatesGR(object)$annotation <- ranges2annot(CTSScoordinatesGR(object), ranges)
+  CTSScoordinatesGR(object)$annotation <- ranges2annot(CTSScoordinatesGR(object), ranges, upstream, downstream)
   
   annot <- sapply( CTSStagCountDF(object)
                  , function(X) tapply(X, CTSScoordinatesGR(object)$annotation, sum))
@@ -443,14 +448,15 @@ setMethod("annotateCTSS", c("CAGEexp", "GRanges"), function (object, ranges){
 #' 
 #' @export
 
-setGeneric("annotateConsensusClusters", function(object, ranges) standardGeneric("annotateConsensusClusters"))
+setGeneric("annotateConsensusClusters", function(object, ranges, upstream=500, downstream=500)
+  standardGeneric("annotateConsensusClusters"))
 
 #' @rdname annotateCTSS
 
-setMethod("annotateConsensusClusters", c("CAGEexp", "GRanges"), function (object, ranges){
+setMethod("annotateConsensusClusters", c("CAGEexp", "GRanges"), function (object, ranges, upstream=500, downstream=500){
   if(is.null(experiments(object)$tagCountMatrix))
     stop("Input does not contain CTSS expressiond data, see ", dQuote("getCTSS()"), ".")
-  consensusClustersGR(object)$annotation <- ranges2annot(consensusClustersGR(object), ranges)
+  consensusClustersGR(object)$annotation <- ranges2annot(consensusClustersGR(object), ranges, upstream, downstream)
   if(!is.null(ranges$gene_name))
     consensusClustersGR(object)$genes    <- ranges2genes(consensusClustersGR(object), ranges)
   validObject(object)
@@ -458,24 +464,28 @@ setMethod("annotateConsensusClusters", c("CAGEexp", "GRanges"), function (object
 })
 
 
-#' @name ranges2annot
+#' Hierarchical annotation of genomic regions.
 #' 
-#' @title Hierarchical annotation of CTSSes
+#' Assigns region types such as `promoter`, `exon` or `unknown` to genomic
+#' regions such as _CTSS_, _tag clusters_, or _consensus clusters_.
 #' 
-#' @description Assigns region types such as `promoter`, `exon` or `unknown`
-#'              to CTSSes.
-#' 
-#' @param ranges A [`CTSS`] object, for example extracted from a
-#'        `RangedSummarizedExperiment` object with the [`rowRanges`]
+#' @param ranges A [`GenomicRanges::GRanges`] object, for example extracted from
+#'        a `RangedSummarizedExperiment` object with the [`rowRanges`]
 #'        command.
 #' 
-#' @param annot A [`GRanges`] from which promoter positions will be inferred.
+#' @param annot A `GRanges` from which promoter positions will be inferred.
 #'        Typically GENCODE.  If the `type` metadata is present, it should
 #'        contain `gene`, `exon` and `transcript` among its values.  Otherwise,
 #'        all entries are considered transcripts. If the `transcript_type`
 #'        metadata is available, the entries that may not be primary products
 #'        (for instance \sQuote{snoRNA}) are discarded.
 #' 
+#' @param upstream Number of bases _upstream_ the start of the transcript models
+#'        to be considered as part of the _promoter region_.
+#'        
+#' @param downstream Number of bases _downstream_ the start of the transcript
+#'        models to be considered as part of the _promoter region_.
+#' 
 #' @return A Run-length-encoded ([`Rle`]) factor of same length as the `CTSS`
 #'         object, indicating if the interval is `promoter`, `exon`, `intron` or
 #'         `unknown`, or just `promoter`, `gene`, `unknown` if the `type`
@@ -507,12 +517,12 @@ setMethod("annotateConsensusClusters", c("CAGEexp", "GRanges"), function (object
 #' gr2 <- gr1
 #' gr2$type            <- c("transcript",     "exon",           "transcript")
 #' gr2$transcript_type <- c("protein_coding", "protein_coding", "miRNA")
-#' CAGEr:::ranges2annot(ctss, gr2)
+#' CAGEr:::ranges2annot(ctss, gr2, up=500, down=20)
 #' 
 #' @importFrom GenomicRanges findOverlaps promoters
 #' @importFrom S4Vectors Rle
 
-ranges2annot <- function(ranges, annot) {
+ranges2annot <- function(ranges, annot, upstream=500, downstream=500) {
   typesWithPromoter <- c( "protein_coding", "processed_transcript", "lincRNA"
                         , "antisense", "processed_pseudogene"
                         , "unprocessed_pseudogene")
@@ -527,7 +537,7 @@ ranges2annot <- function(ranges, annot) {
   
   if(!is.null(annot$type)) {
     classes <- c("promoter", "exon", "intron", "unknown")
-    p <- findOverlapsBool(ranges, promoters(annot[annot$type == "transcript"], 500, 500))
+    p <- findOverlapsBool(ranges, promoters(annot[annot$type == "transcript"], upstream, downstream))
     e <- findOverlapsBool(ranges, annot[annot$type == "exon"])
     t <- findOverlapsBool(ranges, annot[annot$type == "transcript"])
     annot <- sapply( 1:length(ranges), function(i) {
@@ -538,7 +548,7 @@ ranges2annot <- function(ranges, annot) {
     })
   } else {
     classes <- c("promoter", "gene", "unknown")
-    p <- findOverlapsBool(ranges, promoters(annot, 500, 500))
+    p <- findOverlapsBool(ranges, promoters(annot, upstream, downstream))
     g <- findOverlapsBool(ranges, annot)
     annot <- sapply( 1:length(ranges), function(i) {
       if      (p[i]) {classes[1]}
diff --git a/man/annotateCTSS.Rd b/man/annotateCTSS.Rd
index 7ae5d29..7f6771b 100644
--- a/man/annotateCTSS.Rd
+++ b/man/annotateCTSS.Rd
@@ -7,19 +7,25 @@
 \alias{annotateConsensusClusters,CAGEexp,GRanges-method}
 \title{Annotate and compute summary statistics}
 \usage{
-annotateCTSS(object, ranges)
+annotateCTSS(object, ranges, upstream = 500, downstream = 500)
 
-\S4method{annotateCTSS}{CAGEexp,GRanges}(object, ranges)
+\S4method{annotateCTSS}{CAGEexp,GRanges}(object, ranges, upstream = 500, downstream = 500)
 
-annotateConsensusClusters(object, ranges)
+annotateConsensusClusters(object, ranges, upstream = 500, downstream = 500)
 
-\S4method{annotateConsensusClusters}{CAGEexp,GRanges}(object, ranges)
+\S4method{annotateConsensusClusters}{CAGEexp,GRanges}(object, ranges, upstream = 500, downstream = 500)
 }
 \arguments{
 \item{object}{\code{CAGEexp} object.}
 
 \item{ranges}{A \code{\link{GRanges}} object, optionally containing \code{gene_name},
 \code{type} and \code{transcript_type} metadata.}
+
+\item{upstream}{Number of bases \emph{upstream} the start of the transcript models
+to be considered as part of the \emph{promoter region}.}
+
+\item{downstream}{Number of bases \emph{downstream} the start of the transcript
+models to be considered as part of the \emph{promoter region}.}
 }
 \value{
 \code{annotateCTSS} returns the input object with the following
@@ -40,8 +46,8 @@ detected.
 modifications as above.
 }
 \description{
-\code{annotateCTSS} annotates the \emph{CTSS} of a \code{\link{CAGEexp}} object and
-computes annotation statistics.
+\code{annotateCTSS} annotates the \emph{CTSS} of a \code{\link{CAGEexp}} object and computes
+annotation statistics.
 
 \code{annotateConsensusClusters} annotates the \emph{consensus clusters}
 of a CAGEr object.
diff --git a/man/ranges2annot.Rd b/man/ranges2annot.Rd
index 279b971..180c0ed 100644
--- a/man/ranges2annot.Rd
+++ b/man/ranges2annot.Rd
@@ -2,21 +2,27 @@
 % Please edit documentation in R/Annotations.R
 \name{ranges2annot}
 \alias{ranges2annot}
-\title{Hierarchical annotation of CTSSes}
+\title{Hierarchical annotation of genomic regions.}
 \usage{
-ranges2annot(ranges, annot)
+ranges2annot(ranges, annot, upstream = 500, downstream = 500)
 }
 \arguments{
-\item{ranges}{A \code{\link{CTSS}} object, for example extracted from a
-\code{RangedSummarizedExperiment} object with the \code{\link{rowRanges}}
+\item{ranges}{A \code{\link[GenomicRanges:GRanges-class]{GenomicRanges::GRanges}} object, for example extracted from
+a \code{RangedSummarizedExperiment} object with the \code{\link{rowRanges}}
 command.}
 
-\item{annot}{A \code{\link{GRanges}} from which promoter positions will be inferred.
+\item{annot}{A \code{GRanges} from which promoter positions will be inferred.
 Typically GENCODE.  If the \code{type} metadata is present, it should
 contain \code{gene}, \code{exon} and \code{transcript} among its values.  Otherwise,
 all entries are considered transcripts. If the \code{transcript_type}
 metadata is available, the entries that may not be primary products
 (for instance \sQuote{snoRNA}) are discarded.}
+
+\item{upstream}{Number of bases \emph{upstream} the start of the transcript models
+to be considered as part of the \emph{promoter region}.}
+
+\item{downstream}{Number of bases \emph{downstream} the start of the transcript
+models to be considered as part of the \emph{promoter region}.}
 }
 \value{
 A Run-length-encoded (\code{\link{Rle}}) factor of same length as the \code{CTSS}
@@ -25,8 +31,8 @@ object, indicating if the interval is \code{promoter}, \code{exon}, \code{intron
 metadata is absent.
 }
 \description{
-Assigns region types such as \code{promoter}, \code{exon} or \code{unknown}
-to CTSSes.
+Assigns region types such as \code{promoter}, \code{exon} or \code{unknown} to genomic
+regions such as \emph{CTSS}, \emph{tag clusters}, or \emph{consensus clusters}.
 }
 \details{
 Only the biotypes that are likely to have a pol II promoter will be
@@ -49,7 +55,7 @@ CAGEr:::ranges2annot(ctss, gr1)
 gr2 <- gr1
 gr2$type            <- c("transcript",     "exon",           "transcript")
 gr2$transcript_type <- c("protein_coding", "protein_coding", "miRNA")
-CAGEr:::ranges2annot(ctss, gr2)
+CAGEr:::ranges2annot(ctss, gr2, up=500, down=20)
 
 }
 \seealso{